Hi LisaLMT,

You'll want to include the fees when you deposit the payment in QuickBooks, Then, match them with the downloaded transactions in the Banking section.

Here's how:

1. Locate the customer invoices that were paid via Square.
2. Click Create (+), and then Receive Payment.
3. Click Create (+), and then Bank Deposit. 
4. In the Add funds to this deposit section, click the expense account for the fees, and then enter a negative amount.

Once done, you can now match your deposit to the downloaded transactions.

You can check out this article for details: https://squareup.com/help/au/en/article/6081-intuit-quickbooks-sync-with-square-faq.

We're always here if you have any questions. Have a great day.