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. The application does not have the ability to send over just payments either, it will create it's own sales record for the payment to associated with.
For more information on How does sales information appears in my accounting solution? please review the article in the link specific to your scenario.