I have had to go ahead and disable my Shopify integration entirely.  When a Sales Order comes in from Shopify, it lists the shipping charge as a line item with no SKU attached to it.  As you are not able to edit a Sales Orders that comes in from a Marketplace, the shipping charge doesn't get posted to an actual account, and it prevents our API  connections from working as Quickbooks, ShipStation, etc. don't recognize the line item with no SKU.