When posting the second receipt you would not apply to an invoice as that invoice would already be fully paid. You would apply to revenue tab and post ro the Accounts receivable account or Deposit Refunds for the GL. In payments choose the customer that overpaid and issue the check accepting the accounts receivable or Deposit Refunds as the GL account. Once you refund the check, pull up the customer deposit, under the apply to invoice tab you should the check refund amount as the amount due, check the pay box. Click the apply to revenue tab and highlight that row, click Row at the top of receive money window screen and choose remove to remove that line. Now the receipt should be the original amount received and the check amount is applied to that overpayment receipt.