In certain circumstances, payments showing in the Merchant Service Center must be manually created in QuickBooks Desktop. You can create a payment record manually either by receiving a payment or creating a sales receipt and then recording the deposit.
Option 1: Receive the Payment
1. In QuickBooks, choose Customers and then either select Receive Payments or Enter Sales Receipt.
2. Complete the required fields (The card number is optional since the card will not actually be processed).
3. Ensure the Process payment when saving checkbox is clear so the customer's credit card is not actually charged then click Save & Close.
Record the Deposit
1. Choose Banking > Make Deposits.
2. Select the payments on the Payments to Deposit window.
3. Place a checkmark on the payment to deposit then click OK.
4. Select the payments to deposit and update any necessary information and then click Save & Close.