When Square deposits the payments, Commerce Sync will deposit the credit card payments from Undeposited Funds into your bank account in Quickbooks.
The deposit settlement will show all of the payments that are included in the deposit as well as the total amount of Square fees subtracted.
The Square fees are associated to a Square Fees expense account by default.
If there are additional fees such as Square Capital Payments, these get tracked into an expense account called Square Uncategorized Expenses by default.
If there is any additional income such as processing fee rebates, these get tracked into your Square Sales by default.
You can change the deposit accounts in your Commerce Sync settings to redirect these transfer types to another account.
You'll find your deposit information in your bank account in Square. Click on the Chart of Accounts and open the bank account to see this information.