Hi Shelby,
There are a few different ways to handle this. If you entering invoices in QBO for your sales you can take the payment and put it into undeposited funds. As the funds are deposited into your account you select them from the list of items to be deposited and make an adjustment for the merchant fee's as a negative number. Happy to set up a session to review this and other methods in more detail.
Happy Bookkeeping.
Janelle