Workaround that works for me:
1) Set up a "Bank Account" with the name as "Shopify", and record the uploaded payments to this account. It should remain a zero balance.
2) When you do the transaction matching in your bank account, set up a vendor ('alias") as Shopify and use the accounting pre-fill tab on the Vendor Setup to point to this bank account.
The difference between the Shopify payments to your bank and the clients' payments on their invoices becomes instantly visible and easy to write off.
