Is it possible to add a button which would allow you to allocate payments to invoices straight from the customer payment form after each payment is made? It most cases, a remittance advice is attached to the cheque and it would be much easier to post the payment, then automatically have the option to apply said deposit to the invoices. A button at the bottom of the payment page could link to the allocation form and, when finished, return you to the payment form to enter the next payment.

Judging by some of the questions/issues I've seen in the forums, this feature would help eliminate some of the confusion as to why invoices are still showing as unpaid after a deposit is made because of the separation between payment and invoice allocation.