This system wide Sales Default setting in weintegrate controls whether QBO or Shopify assigns the transaction number in QBO for the Shopify sales document being posted.
This dropdown is preset to QuickBooks Online, but you may opt to change it to Shopify.
If you set this value to QuickBooks Online, then QBO will auto-assign the Sales Receipt number based on your current setting within QBO.
If you set this value to Shopify, then the Sales Receipt number in QBO will be populated with the Shopify sales transaction number.
The Sales Default screen is available in both the Configuration Setup Wizard and the Connection management section of the app.
Click here to learn about setting the Shipping Date default for integrating with QuickBooks Online.