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You have installed the qmail-activedir.

Now you need follow this steps:

1) create the control files.

2.a) Test

# %%QMAIL_PREFIX%%/bin/qmail-popup blah %%PREFIX%%/bin/checkadpassword id

Put in a valid username and password and it should give you the results of id.
Do the same with pwd to make sure that the user, group and directory are 
correct.

Do it again with an invalid username and password to verify that it will
actually reject failures.

Check the auth log to verify that the failure occurred.

2.b) Test some more

Next test the ad_getpw:

# %%PREFIX%%/bin/ad_getpw user
It should return the user, uid, gid, homedir, separated by NULL character

2.c) Just using create_alias_files will let you know if it works...
Do %%PREFIX%%/bin/create_alias_files -h for more info.

3) Copy the original someplace and rename:
# mv %%QMAIL_PREFIX%%/bin/qmail-getpw %%QMAIL_PREFIX%%/bin/qmail-getpw_old
# cp %%PREFIX%%/bin/qmail-adgetpw %%QMAIL_PREFIX%%/bin/qmail-getpw

4) Update your qmail pop scripts (run file) like this:
...
%%QMAIL_PREFIX%%/bin/qmail-popup "${POPUPHOST-`sed 1q %%QMAIL_PREFIX%%/control/me`}" \
%%PREFIX%%/checkadpassword \
%%QMAIL_PREFIX%%/bin/qmail-pop3d "${MAILDIRNAME-Maildir}"
...

and restart.  Run some trial tests.

For more information you should read %%DOCSDIR%%/README.