Do I have to set these accounts set up differently? I am about to set up the school as fund 02 and don't want to totally mess things up!

From reading some other posts it sounds like I may have things totally messed up. Everything for the church is set up under fund 01 regardless of what checking account pays those bills, and everything for the school will be entered under fund 02 and paid out of the school's checking account.
If I do have things set up right, how do I tell PC+ (version 10) which checking account I am paying a bill out of? I don't see that anywhere. If I have things set up wrong how do I fix it?
