When syncing orders from Shopify into QuickBooks Online as invoices or sales receipts, MyWorks will record the payment in QuickBooks Online as long as the Shopify order is paid.

You can control how the order and payment are synced to QuickBooks Online for paid orders in MyWorks Sync > Settings > Payment Methods, separately for each payment method you offer in your Shopify store! 

Once you visit MyWorks Sync > Settings > Payment Methods, you'll see a section on the page for each payment method present in your store. This includes the default Shopify Payments option and any custom payment methods you have present on your store for recent orders. Additionally, the last section is named “Other” to apply to any orders that have no payment method in Shopify.

 
In this area, you can control:

• The QuickBook “Payment Method” label used as the Payment Method in QuickBooks
• The Bank Account in QuickBooks that these payments should be recorded to - based on location and currency (if applicable) in your Shopify store
• Syncing the transaction fee in the QuickBooks order (if present in the Shopify order. This is available for Shopify Payments only.)
• Syncing refunds from Shopify to QuickBooks