If you didn't record the account fees when you deposited the credit card
payments, write an expense check to account for the fees.
Note: If you have a QuickBooks Point of Sale Merchant Account, you can also use this method.
Go to the Banking menu and click Write Checks.
Click the Bank Account drop-down list and choose the bank account that is used
by your merchant account processor for your credit card transactions.
Click the Pay to the Order drop-down list and choose a vendor name that you have
set up for your merchant account processor.
Delete the check number. In its place, enter a note to indicate that this
check is actually a deduction for merchant account fees, such as MDF.
Enter the total amount of the fees.
Clear the To be printed checkbox.
On the Expense tab, choose the account that you are charging for the
transaction, such as Bank Charges or Merchant Account Fees.
Save the check.
The Merchant Service for QuickBooks makes it easier for you to account for the difference between your QuickBooks deposit total and the deposit total on your bank statement.