For Shopify stores on Shopify Plus, Shopify includes a system field named “PO Number” in orders placed by a customer within a “Company” on your Shopify store. When this is present, MyWorks supports syncing this PO Number field in Shopify orders into a custom field of your choice in QuickBooks.

This can be easily set in MyWorks Sync > Map > Custom Fields, as shown in the example below.  

Not on Shopify Plus? It's still possible to add a Metafield to your Shopify order and map that to a field in the QuickBooks order in the same way.