Not sure if this is implemented or not, but I was hoping there was a way to mark an invoice as paid in the admin area. We have users who like to send checks, so once the check clears we can go in and change there invoice status to paid. Is this not a feature?
I submitted a trouble ticket regarding this issue. The development team is working on this and new features as well. Until then, I have been using phpMyadmin to mark items paid directly in the database. Its a quick workaround until the new updates come out.