Hello there, mistergiant. The 2.99% fee is automatically deducted from the payment before it reaches your bank account, which is why your actual deposit is the net amount (the total minus the fee). The invoice still shows the full amount to confirm that your client has paid their balance in full.
You can sign in to QuickBooks Payments to view the fees. Go to the Activity & Reports tab and select Deposits. Look for the Fee column to see the amount deducted for that transaction.
Feel free to return to this thread if you have follow-up questions.