Commerce Sync transfers the refunds that happen in your point of sale or payment solution. The refunds typically transfer as a separate transaction from the invoice. Refunds transfer differently depending on your point of sale, payment solution and QuickBooks version. For the most part, you will see either a Refund Receipt or Credit Memo in QuickBooks when it is transferred.
Here is the setting in the Commerce Sync Dashboard:
The accounts, items, and customers in your Commerce Sync settings are populated by the information Commerce Sync receives from QuickBooks. Commerce Sync will create place-holder items and accounts to use when you install and connect to QuickBooks.