MyWorks includes the ability to sync the transaction fee charged to you by Shopify within each order as we sync the order into QuickBooks: as a negative line item in the QuickBooks order. This is available for orders paid by Shopify Payments.
 

This can be easily set up in MyWorks Sync > Map > Payment Methods:

1. In QuickBooks, create a non-inventory or service item to be used as the line item for transaction fees in orders we sync. The QuickBooks account this item should be assigned to would be your transaction fees expense account.
    
2. In MyWorks Sync > Map > Payment Methods, enable the setting to sync transaction fees.

Then, in orders synced to QuickBooks, the transaction fee will be present as a line item, and the order/payment total in QuickBooks would be the “net” amount you receive from the Shopify order.