Payments are applied to the invoice to close the invoice as paid. These payments will be separated by the tender type that is accepted in your Square account.
By default, all of the payments are associated to your Undeposited Funds account. You can open your Undeposited Funds account by going to the Chart of Accounts and double-clicking the Undeposited Funds account.
Credit Cards - payments are broken down by individual transactions in QuickBooks, these will always be associated to your Undeposited Funds account. Commerce Sync will then reconcile your Payments to Deposit when your Square credit card deposit information is transferred.
Cash, Checks and Other Payment Types - are transferred as a summarized payment in QuickBooks, one for each of these payment types that you use. These will be associated to your Undeposited Funds account by default. You can change the Clearing Account in your Commerce Sync settings to map these payments types to another account moving forward. Commerce Sync does not reconcile your Cash, Check or other Payments to Deposit.
Square fees will transfer into your company file when the Square Deposit information is transferred by Commerce Sync.