You can record overpayments in MechanicDesk in several different ways depending on your accounting needs. 

(a) You can create a new payment record for the customer and allocate it to the correct invoices. 1 payment record can have multiple invoice associations. Any remaining payments are listed as unallocated and will appear in the customer's balance information.

(b) Invoice the correct amount anyway and put the remainder into credit for the customer. The invoice will not show any overpayment information. To put in credit for a customer, please refer to the Credit Note facility.

Please contact the MechanicDesk support team if in doubt.