There are two ways to add discounts to a QuickBooks invoice: the "discount feature" or "discount as an item". The best explanation of the options is here: https://quickbooks.intuit.com/learn-support/en-us/service-items/apply-a-discount-on-an-invoice-or-sales-receipt/00/186357
If you choose to use the "discount as an item" approach, you can select that item (once you've created it in QuickBooks) in the patient's chart/encounter, in the "Plan" section where you see "Other Items". Just type the name of the discount item and select it from the auto-complete, and set the amount of the discount (be sure to use a negative number).