Three different entities sounds like three times the work. Have you considered using qualifiers? You can add qualifiers to your accounts for each of your departments and then run reports based on those qualifiers, while still continuing to use the same checkbook.

If you need information about qualifiers, there is a lot of documentation in the FN Help System and the Reference Guide Volume 1 (page 74).

For the FN Help System:
1. Click the Help button in FN to launch the Help System.
2. Under the Index tab, search for the words: Account Qualifiers. Look for the topic "Account Qualifiers – Overview" for a good starting point.

Let us know if this does not solve your problem.