I always create an invoice for a non-inventory item "over payment" before I post the check. I use the check number for the PO. After posting the full payment (including the over payment invoice) I create a credit memo that I can share as an actual credit memo with an actual balance that I can send to the customer to either keep on account or request a refund.  All of my customers require an actual numbered credit memos. Stupid, I know, QB versions ago used to ask if you wanted to create a credit memo for the over payment,but they dropped that simple option for some unknown reason and refuse to put it back