Janine is right on the way (partial) shipments are handled in by the ecommerce package. Each individual item that has been shipped is marked as 'shipped' and its shipment_id is set to the ID of the shipment that it is part of.
The shipped items are marked by fulfill-3.tcl in ecommerce/www/admin/orders. Take a look at the whole series of fulfill-* files for a complete overview of how shipments are handled.
