Cindy:
We do have an API (Payment Gateway) that you can write code around that will process transactions and store those transactions in F1 - so that you can report on them, etc... That would give you the greatest flexibility, however, I get the impression that you may be looking for some specific features.
We are beginning to architect a new foundation for Payment Processing so that it can be used in many different ways. We would love to hear your thoughts / suggestions on what you and others around you would like to see in any new payment functionality that we are planning on developing! (You mentioned that you have to modify the way you do things around payments - if you have a moment please elaborate)
Thanks for taking the time to make the Church world better!
--Nick