From the QuickBooks users guide.
To write a refund check:
When you need to refund a customer some money, create a credit memo first. Then you can write a refund check.
Open the credit memo you want to use for the refund.
Click Refund at the top of the window.
Make sure all the information on the check is correct.
Caution: Leave Accounts Receivable as the account in the detail area of the refund check. This ensures that QuickBooks will account for the credit and refund correctly.
Although you have recorded both the credit memo and the check, you still need to connect the check to the credit memo so that QuickBooks can track the transaction correctly. You use the Receive Payments window to connect the two.
To connect the refund check to the credit memo:
1 Choose Customers > Receive Payments.
2 Choose the customer to whom you just wrote the refund check. You'll see the amount of the credit
included in the Existing Credits field and the refund check in the bottom section of the window.
3 Select the Apply Existing Credits checkbox.
4 On the Refund Chk line, enter the check amount in the Payment column, if not already entered by QuickBooks, and then click OK. If you now choose Customers > Create Credit Memos/Refunds to display the credit memo you just entered and click Tx History, you should see the refund check listed in the Transaction History - Credit memo window.