Hi Ben621. 

I'm happy to help, what you're going to want to do is set up class tracking, set up categories for expenses and accounts and filter/sort total reports by class. This will make it easier to generate reports to compare multiple departments you previously mentioned. 

Here's how:

Turn on Class Tracking:

1. Open your company file.
2. Go to the Edit menu, then select Preferences.
3. Select Accounting, then go to the Company Preferences tab.
4. Select the Use class tracking for transactions checkbox.
5. If you want a reminder when you haven't assigned a class, select the Prompt to assign classes checkbox.
6. Select OK.

Set up categories for expenses and accounts:

1. Go to the Lists menu, then select Class List.
2. From the Class ▼ drop-down menu, select New.
3. Enter the class name.
4. If it's a subclass, select the Subclass of checkbox and find the class it's under in.
5. Select OK to add it.

To filter, sort and total reports by class for departments, refer to that article. Also, if you happen to be using a mac or want more information on the steps above, check out this helpful article. 

If there's anything else I can help with, feel free to post down below. 

Thanks for your time and have a nice weekend.