If you have discounts in your point of sale or payment system, you can turn this feature turned on to track your discounted sales in QuickBooks.
You will see the discounts as a line on the invoice Commerce Sync transfers. The Discounts account in QuickBooks will be in Income account, so that your QuickBooks reports (Profit and Loss, Balance Sheet, etc.) will accurately reflect sales vs. discounts.
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.