Commerce Sync is a one way transfer of information from your point of sale or payment solution into your accounting solution.
Every day, Commerce Sync will create an invoice using the information in your settings to map to in QuickBooks or Xero. The application does not apply payments to invoices that you already have created in QuickBooks or Xero.
For more information on How does sales information appear in my accounting solution? please review the article in the link specific to you scenario.