Hey!

Here is what worked for me.

On the banking tab, download your bank transactions to quickbooks.

In there, you'll find the correct deposit amount (For example, $3540.00).

Click on it and then click on "Find match".

When you do that, you'll be shown a new screen with payments you have received within a certain period of time. Find the payment and select it.

Quickbook will tell you that you can't match it, because the amount doesn't match.

All the way to the bottom, there's a little switch that says "Resolve", once you click on that, a new line will pop-up at the bottom and you can add the merchant fee in there -- make sure you put it as a negative amount.