Hello Bosskoss,

When managing transactions from Square and other platforms, they have to go through the Banking page. From there, they'll be added or matched to transactions on your QuickBooks register.

Before the transactions (Square and other platforms) reached or cleared on your bank, the amounts were usually deducted by the service fees. Hence, the amounts are in the Banking page are lesser than what you have on your QuickBooks. With that said, we have a process in QuickBooks on how to deposit the sales transactions that will match to the Banking page.

Under the Step 2 on this article, you can include the processing fee: Record and make Bank Deposits in QuickBooks Online.

After creating the deposit, that's the time we can match the transactions.

Feel free to get back to me if you have additional queries on how manage these transactions. Have a great day!