I did some research and found the solution to making sure that fee is accounted for. You can follow these steps when depositing the payment from the Intuit Payments Services.

• Go to the Plus "+" and select Bank Deposits.
• You should see the payment in the Select Existing Payments section. 
• Place a checkmark to select the payment to deposit.
• Under the Add New Deposits section enter the fee charged to you as a negative amount.
• Under the Account section, select the Expense account you use to track these fees.
• Verify that the deposit amount is correct.
• Then click Save.

Please let me know how this goes for you.