Yes, you can do just as you describe. If you are running CheckBook Pro, you can click on the 'All Accounts' section in the Accounts drawer, then click on the Summary tab at the bottom of the window. From the summary tab, you can create a new summary for the entire year with a monthly subtotal of categories. This will show the totals of your spending per category for each month and include entries from all of your accounts.
If you have not done so, you can try all of this yourself with the free trial of CheckBook Pro. You can find CheckBook Pro here:
http://www.splasm.com/checkbookpro/downloads.htmlThis is the best way to find out if this is the solution you are looking for. Thanks for the question, Deb!