1. Is the invoice paid in another customer code
2. Is there an invoice unrecorded that my turn up later
3. Is the effect on overstating the inventory quantity and value important to adjust (and conversely to Cost of Sales)
4. Is the customer taxable and the amount of sales tax needs to be paid to the state
5. Is the overpayment on the account as an unapplied payment, applied to the wrong invoice or something else

After satisfying that #1-4 above are not an issue

1. The amount for which payments are paid in full should be recorded in full as a normal payment code (eg. 40)
2. The amount paid in excess of invoices should be processed as an unapplied credit (eg. 60 code) on a separate transaction.
3. The customer should be contacted by phone, fax or email asking for a copy of the invoice that they are paying that is not in their customer account.