CHECKFREE HOLDINGS CORP
SC 13G/A, 2000-02-14
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<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                 SCHEDULE 13G/A
                                 (Rule 13d-102)

             INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
           TO RULES 13d-1(b)(c), AND (d) AND AMENDMENTS THERETO FILED
                            PURSUANT TO RULE 13d-2(b)
                              (Amendment No. 1)(1)


                         CHECKFREE HOLDINGS CORPORATION
- --------------------------------------------------------------------------------
                                (NAME OF ISSUER)

                          COMMON STOCK, $.01 PAR VALUE
- --------------------------------------------------------------------------------
                         (TITLE OF CLASS OF SECURITIES)


                                   162816 10 2
- --------------------------------------------------------------------------------
                                 (CUSIP NUMBER)



                                FEBRUARY 7, 2000
- --------------------------------------------------------------------------------
                      (DATE OF EVENT WHICH REQUIRES FILING
                               OF THIS STATEMENT)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

     [ ]  Rule 13d-1(b)

     [X]  Rule 13d-1(c)

     [ ]  Rule 13d-1(d)

(1) The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter disclosures provided in a prior cover page.

        The information required on the remainder of this cover page shall not
be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange
Act of 1934 ("Act") or otherwise subject to the liabilities of that section of
the Act but shall be subject to all other provisions of the Act (however, see
the Notes).

                         (Continued on following pages)
                               (Page 1 of 7 Pages)


<PAGE>   2

- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 2 of 7
- ---------------------                                          -----------------

- -------------------------------------------------------------------------------
   1      NAME OF REPORTING PERSONS
          I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

          INTUIT INC. - 77-0034661
- -------------------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP              (a)  [ ]
                                                                        (b)  [X]
- -------------------------------------------------------------------------------
   3      SEC USE ONLY
- -------------------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
          DELAWARE
- -------------------------------------------------------------------------------
                        5      SOLE VOTING POWER
     NUMBER OF                 -0-
      SHARES           --------------------------------------------------------
    BENEFICIALLY        6      SHARED VOTING POWER
      OWNED BY                 10,175,000 (1)
     REPORTING         --------------------------------------------------------
    PERSON WITH         7      SOLE DISPOSITIVE POWER
                               -0-
                       --------------------------------------------------------
                        8      SHARED DISPOSITIVE POWER
                               10,175,000 (1)
- -------------------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
          10,175,000 (1)
- -------------------------------------------------------------------------------
  10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 9 EXCLUDES CERTAIN
          SHARES                                                             [ ]
- -------------------------------------------------------------------------------
  11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
          19.5%
- -------------------------------------------------------------------------------
  12      TYPE OF REPORTING PERSON
          CO
- -------------------------------------------------------------------------------

(1) Shared only by virtue of the fact that Intuit Ventures Inc. ("IVI"), the
record holder of the shares, is a wholly-owned subsidiary of Intuit Inc.
("Intuit"). Intuit disclaims beneficial ownership of the shares under Rule
13d-3.


<PAGE>   3

- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 3 of 7
- ---------------------                                          -----------------

- -------------------------------------------------------------------------------
   1      NAME OF REPORTING PERSONS
          I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

          INTUIT VENTURES INC. - 94-3346525
- -------------------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP              (a)  [ ]
                                                                        (b)  [X]
- -------------------------------------------------------------------------------
   3      SEC USE ONLY
- -------------------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
          DELAWARE
- -------------------------------------------------------------------------------
                        5      SOLE VOTING POWER
     NUMBER OF                 -0-
      SHARES           --------------------------------------------------------
    BENEFICIALLY        6      SHARED VOTING POWER
      OWNED BY                 10,175,000 (2)
     REPORTING         --------------------------------------------------------
    PERSON WITH         7      SOLE DISPOSITIVE POWER
                               -0-
                       --------------------------------------------------------
                        8      SHARED DISPOSITIVE POWER
                               10,175,000 (2)
- -------------------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
          10,175,000 (2)
- -------------------------------------------------------------------------------
  10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW 9 EXCLUDES CERTAIN
          SHARES                                                             [ ]
- -------------------------------------------------------------------------------
  11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
          19.5%
- -------------------------------------------------------------------------------
  12      TYPE OF REPORTING PERSON
          CO
- -------------------------------------------------------------------------------

(2) Shared only by virtue of the fact that IVI is a wholly owned subsidiary of
Intuit.


<PAGE>   4

- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 4 of 7
- ---------------------                                          -----------------

ITEM 1(a).     NAME OF ISSUER:
               CheckFree Holdings, Inc., a Delaware corporation

ITEM 1(b).     ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:
               4411 East Jones Bridge Road
               Norcross, Georgia, 30092

ITEM 2(a).     NAME OF PERSON FILING:
               (i)    Intuit Inc.
               (ii)   Intuit Ventures Inc.

ITEM 2(b).     ADDRESS OF PRINCIPAL BUSINESS OFFICE OR, IF NONE, RESIDENCE:
               (i) 2535 Garcia Avenue
               Mountain View, California  94043

               (ii)1285 Financial Boulevard
               Reno, Nevada 89502-7103


ITEM 2(c).     PLACE OF ORGANIZATION OR CITIZENSHIP:
               (i) and (ii):  Delaware

ITEM 2(d).     TITLE OF CLASS OF SECURITIES:
               Common Stock, par value $.01 per share

ITEM 2(e).     CUSIP NUMBER:
               162816 10 2 (CheckFree)

ITEM 3.        IF THIS STATEMENT IS FILED PURSUANT TO RULE 13-d-1(b), OR
               13d-2(b) OR (c), CHECK WHETHER THE PERSON FILING IS A:

               (a)    [ ]   Broker or dealer registered under Section 15 of
                            the Exchange Act;

               (b)    [ ]   Bank as defined in Section 3(a)(6) of the Exchange
                            Act;

               (c)    [ ]   Insurance company as defined in Section 3(a)(19)
                            of the Exchange Act;

               (d)    [ ]   Investment company registered under Section 8 of
                            the Investment Company Act;

               (e)    [ ]   Investment adviser in accordance with Rule
                            13d-1(b)(1)(ii)(E);

               (f)    [ ]   An employee benefit plan or endowment fund in
                            accordance with Rule 13-d-1(b)(1)(ii)(F);

<PAGE>   5
- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 5 of 7
- ---------------------                                          -----------------

               (g)    [ ]   A parent holding company or control person in
                            accordance with Rule 13d-1(b)(1)(ii)(G);

               (h)    [ ]   A savings association as defined in Section 3(b)
                            of the Federal Deposit Insurance Act;

               (i)    [ ]   A church plan that is excluded from the
                            definition of an investment company under Section
                            3(c)(14) of the Investment Company Act;

               (j)    [ ]   Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

               If this statement is filed pursuant to Rule 13d-1(c), check this
               box.   [X]

ITEM 4.        OWNERSHIP:



               (a)   Amount beneficially owned:
                     10,175,000 Intuit has contributed to its subsidiary IVI all
                     10,175,000 shares of the Common Stock of CheckFree Holdings
                     Corporation previously beneficially owned by Intuit. Intuit
                     owns 100% of the issued and outstanding capital stock of
                     IVI. This transfer was effected in conjunction with other
                     contributions to IVI of equity securities in Intuit's
                     investment portfolio.

               (b)   Percent of class:
                     19.5%

               (c)   Number of shares as to which such person has:

               (i)   Sole power to vote or to direct the vote: -0-

               (ii)  Shared power to vote or to direct the vote: 10,175,000
                     Shared only by virtue of the fact that IVI is a wholly
                     owned subsidiary of Intuit. Intuit disclaims beneficial
                     ownership of the shares under Rule 13d-3.

               (iii) Sole power to dispose of or to direct the disposition of:
                     -0-

               (iv)  Shared power to dispose of or to direct the disposition of:
                     10,175,000 Shared only by virtue of the fact that IVI is a
                     wholly owned subsidiary of Intuit. Intuit disclaims
                     beneficial ownership of the shares under Rule 13d-3.


ITEM 5.        OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS:
               Not applicable

ITEM 6.        OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON:
               Not applicable
<PAGE>   6
- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 6 of 7
- ---------------------                                          -----------------

ITEM 7.        IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
               ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING
               COMPANY:
               Not applicable


ITEM 8.        IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP:
               Not applicable

ITEM 9.        NOTICE OF DISSOLUTION OF GROUP:
               Not applicable

ITEM 10.       CERTIFICATIONS:


Because this statement is filed pursuant to Rule 13d-1(c), the following
certification is included:

        By signing below, we certify that, to the best of our knowledge and
belief, the securities referred to above were not acquired and are not held for
the purpose of or with the effect of changing or influencing the control of the
issuer of the securities and were not acquired and are not held in connection
with or as a participant in any transaction having that purpose or effect.

                                    SIGNATURE


After reasonable inquiry and to the best of our knowledge and belief, we certify
that the information set forth in this statement is true, complete and correct.

Date:  February 14, 2000

                                            Intuit Inc.


                                            /s/ Greg J. Santora
                                            --------------------------
                                            Greg J. Santora
                                            Senior Vice President and
                                            Chief Financial Officer


                                            Intuit Ventures Inc.


                                            /s/ Barry Simcoe
                                            --------------------------
                                            Barry Simcoe
                                            President


<PAGE>   7
- ---------------------                                          -----------------
CUSIP NO. 162816 10 2                   13G/A                     Page 7 of 7
- ---------------------                                          -----------------

                             JOINT FILING AGREEMENT

        In accordance with Rule 13d-1(k)(1) under the Securities Exchange Act of
1934, as amended, the undersigned hereby agree to the joint filing with each
other of the attached statement on Schedule 13G/A relating to the shares of
common stock of CheckFree Holdings Corporation held by each of the undersigned
and to all amendments to such statement.

        IN WITNESS WHEREOF, the undersigned hereby execute this agreement on
February 14, 2000.

                                            Intuit Inc.


                                            /s/ Greg J. Santora
                                            --------------------------
                                            Greg J. Santora
                                            Senior Vice President and
                                            Chief Financial Officer


                                            Intuit Ventures Inc.


                                            /s/ Barry Simcoe
                                            --------------------------
                                            Barry Simcoe
                                            President


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