Invoice Management?
First - A simple idea really. The ability to select paid invoices and "hide" them from the invoices that are already paid. - OR - a simple tick box at the top of the invoice screen that can switch from Open Invoices and Paid Invoices.
Second - On the min Invoice screen, show the amount owed instead of having to select the individual invoice then looking there. It would streamline everything a lot better and you wont have to leave a customer on hold for an additional 10 seconds while you look for the balance on the individual Invoice. Just have all the balances owed right on the invoice screen.