How to ship an order with two line items with two separate labels.
Select just one line item and generate a label. In this example, we ship the 1st line item only, so we uncheck the second line item.
Click submit tracking to market.
This will create a shipment and you will see that a line item is shipped.
Generate the 2nd label.
And also submit this label to Marketplace.
You will now see two labels and two shipments, and both line items marked as shipped: