When syncing orders from Shopify into QuickBooks Desktop as invoices, sales receipts, or sales orders, MyWorks can record a payment for the order in QuickBooks Desktop as long as the Shopify order is paid.

You can control how the payment is synced to QuickBooks Desktop 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 in your store. This includes the default Shopify Payments option and 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 only available for Shopify Payments orders.)
• Setting a specific Term for the invoice in QuickBooks, if unpaid