If you have a situation where a member has been invoiced and paid an amount that was incorrect, and therefore requires a refund rather than just a credit on account you can do the following:
As the balance for the overpayment is currently zero (example: an invoice was raised for $100 and a payment was made for $100 and allocated to that invoice amount), you first need to credit the invoice for the amount of the overpayment which will create a credit on the member's account. See CREDITING AN INVOICE or CREATING A CREDIT INVOICE to do this step.
Once you have a credit on account, you can then add a negative payment to the account by selecting the Payment button from the Invoicing> Accounts Receivable module, and entering a negative number. In the reference - you can explain this was a payment refund if you wish. Allocate the negative amount against the credit invoice which should display below. This will balance the member account back to zero and also provide the relevant data to balance your revenue account and payment accounts when you export to your financial software.