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
 Receiving Payment of Account in Blackpurl (Accounting Integration)

Step 2. for the over paid amount you would 
  1. On the Blackpurl Header > SELL
  2. Do not select the type of Customer Order > just add the customer
  3. click deposit
  4. receipt the payment using the same payment method as you received payment ie Cheque and Cheque
  5. Then do a refund using Store Credits as the payment method
  6. 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.