When syncing orders from Shopify into QuickBooks Online as an invoice or sales receipt, 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 > Map > Payment Methods, separately for each payment method you offer in your Shopify store! 

Once you visit MyWorks Sync > Map > Payment Methods, you'll see a section on the page for each payment method present on your store. This includes the default Shopify Payments option, as well as any custom payment methods you have in place. Additionally, the last section is named “Other” - to apply to any orders that don't have a payment method in Shopify.

 
Here, you can control:

• The “Payment Method” label used for payments in QuickBooks
• The Bank Account in QuickBooks that these payments should be recorded to
• Syncing the transaction fee in the QuickBooks order (if present in the Shopify order. This is normally for Shopify Payments orders.)
• Setting a specific Term for the invoice in QuickBooks, if unpaid