Customer has had an invoice charged on account and then sends in a payment which is more than they owe.
Step 1. Receive the payment due on the Customer record
Step 2. for the over paid amount you would
On the Blackpurl Header > SELL
Do not select the type of Customer Order > just add the customer
receipt the payment using the same payment method as you received payment ie Cheque and Cheque
Then do a refund using Store Credits as the payment method
The CO will automatically closed when you do the refund
This then puts the funds to undeposited funds in your accounting package to balance out the full amount of the cheque/funds received and shows the Store credit as a liability which it should be until utilised.