This system wide Sales Default setting controls what document type will be created within QuickBooks Online (QBO) for the Shopify sales being integrated. The current version of weintegrate only supports creating a Sales Receipt within QBO, therefore there are no options for you to select here.
A future release will add the ability for you to opt between Sales Receipts and Invoices in QBO.
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 Deposit Payment to account default for integrating with QuickBooks Online.