MyWorks supports syncing Shopify orders that contain discounts in several ways.

Using the “Discount” subtotal field in QuickBooks

This is how MyWorks handles order discounts by default. Any discounts in the Shopify order will show in the QuickBooks order's “Discount” subtotal field, as in the below example. 

Syncing the discount within the line item

Coming soon! For cases where the discount in the Shopify order is reflected in one or more of the line items in the order, MyWorks can be configured to instead reflect the discount within each line item in the order in QuickBooks, showing the line item in QuickBooks as the “net” amount after the discount.