When processing invoice payments through QuickBooks Merchants Services, the ability to add credit card processing fee manually isn't applicable. The fee is automatically charged every time you do a transaction.
You can visit our QuickBooks Payments website for the most latest rates per transaction. Just a heads-up, fees may vary and subject to change.
To learn more how credit card processing fee works in QuickBooks, you can read through these articles:
Happy to provide some insight into merchant processing fees in QuickBooks. The fee isn't passed onto the customer due to state and federal regulations. The customers won't see this fee, but you'll see it on your end when the payment is processed. It will be deducted from the total payment that the customer makes before being deposited to your bank account.
For more information on processing fees, you can refer to the links provided by @juVielL above.
Let me know if you have any other questions. I'm here to help.