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 once the Shopify order has been paid — in full or in part.
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
Orders that are only partially paid
If you capture part of an order's total in Shopify — a deposit up front, the balance on delivery — Shopify marks the order as partially paid. MyWorks records each capture in QuickBooks as its own payment, dated when the money arrived, for the amount taken. When you collect the balance later, only the balance syncs; the deposit already in QuickBooks is left alone.
Every payment carries the Shopify order number as its reference, so all the payments on one order are easy to find together. Your Sync Log names them in order — “Payment 1 of 2”, “Payment 2 of 2”.
This applies to orders syncing as an invoice or a sales order. Sales receipts already include the payment in the receipt itself, so no separate payment is recorded.
Worth checking: partially paid orders have to be syncing in the first place. In MyWorks Sync > Settings > Orders, look at “Automatically sync orders when they reach any of these statuses”. If Partially paid isn't ticked, those orders don't sync at all — and no payment will be recorded until the order is fully paid.