Using software for Ministry with church under it

[Hisprazr]

We are using the software for a religious organization with a church under the main ministry. Lets say Ministry name is A, Counseling center under that and Church as well.
We only have one bank account but I need to make sure I can differentiate which money is coming and going from each entity but still have the one main bank account. Right now I have Ministry A bank account as the only bank account and everything comes into it. But, when I pay bills I want to be able to take those for the church out of a different account than the ones for the counseling center and main office. I have thought of different ways but not sure how they would work with the other parts of the system to give the correct figures. Have any ideas?

[JohnDMeyers]

I think you would want to have a separate Accounting Fund for your Counseling center.

You can still have one (physical) bank account. Use the same 4-digit major account number for both, like this:

Fund 01
01-1110-000 General checking

Fund 02
02-1110-000 Counseling Center checking

When you reconcile the bank account, using 1110 will bring up all the checks from both Funds.