Sure, you'll need a submit data connection for each folder you can potentially submit to. Once you've created all of these DCs, you can use rules to check what department the info form is for and submit to using the proper connection. You'll also need to have a submit button as this is the best way to run rules on submit instead of using the ribbon submit.
Hope this guides you in the right direction, but if you need more specifics on how to do this let me know and I can walk you through it.