QuickBooks will not allow you to make a negative deposit. If you want to record a deposit when your credit card refunds are greater than your payments, try the following procedure.
Create a new account with a type of Other Current Asset. (This account will be used as a temporary clearing account. There will be a transaction entered in this register, although the amount will be zero.)
In the Payments to Deposit window, select the payments and refunds you want to deposit, as you usually do.
On the Make Deposits screen, instead of depositing to the account you normally use, change the Deposit To field to the clearing account you created in step 1.
On the last line of the deposit, select your checking account in the From Account field, and enter the amount necessary to zero out the deposit.
When the Deposit Subtotal is zero, save the transaction.
This will create a negative deposit in your bank account for the correct amount. The clearing account you created will show the transaction but will have an amount of zero. This clearing account should never have a balance.
If the Payments to Deposit window opens, select the payment(s) you would like to deposit now and click OK.
In the Make Deposits window, select the bank account for the deposit.
Click anywhere below the last payment in the list to add an entry. (If the list is full, click anywhere in the list and press Ctrl+Ins to add another line).
In the From Account column, select the expense account from the pull-down list to be associated with the fees.
Enter the amount of the fee as a negative number in the amount field.
When receiving payment from a customer, use the undeposited funds account. This will serve as a placeholder for your funds until they get deposited as a group into your bank. Once you make a deposit at the bank, go to make deposits in QuickBooks and select the payments that were in your deposit.
This will ensure your bank statement deposits match the deposits made in QuickBooks