Unapplied Cash from Cash Receipts

Have any users found a way to link information, that is known when entering a cash receipt, to unapplied cash created from that cash receipt?

Let me explain.  We have many situations where we receive payments from customers where they detail the reason for their payment, but we have no matching transactions open in AR.  Perhaps they are paying an invoice that was previously paid, or making a payment referencing a number that is not on the open invoice.  Today, all amounts overpaid on their payment are totalled in one "lump", with no way for us to detail the information that the customer gave us on their remittance advice.  Currently, we are taking the total unapplied and entering individual standalone chargebacks, since we then can