You can use the Edit Shipments features to achieve this. You can then create additional shipments for your different boxes and purchase labels for each shipment. The only caveat at present is that you can only create additional shipments as long as not all items on the order has been assigned to a shipment, once all items have been assigned to a shipment and those shipments have labels purchase you cannot create more shipments to purchase more labels. The latter we are working on adding support for in a future release.