If you use the Square Gift Card app, this activity is tracked with a Gift Card line item on the invoice, a line each for the purchase of a gift card and the redemption of a gift card. The purchase, redemption and refund of a sale associated to Gift Card transaction are reported in the Gift Card Liability Account in QuickBooks.
Please reach out to email@example.com if you'd like to understand how gift cards transfer that is not from the Square Gift Card app or for any other point of sale/payment solution.
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.