You could allow invoices to be overpaid:
1. Navigate to System Management > Company Maintenance > Company.
2. Navigate to the Modules > All Modules > Localization > Detail sheet.
3. Under AR Invoice Overpayment, select Allow Invoices to be overpaid. This allows the over-allocation of cash against an invoice, leaving it with a credit balance. The overpayment is left as a balance on the same chart of account (usually AR Chart of Account) as if it were an invoice. AR Apply Credit Memo and Write-off, and Adjustment routines allow application or write-off of an invoice overpayment.