We have a product that ships in two boxes, so what do we do when we print out the label for the order and there is only one label?
Store Manager will only create one label at the cost defined by the product weight. As a result, you will have to do the shipping outside of Store Manager.
In this case, I would process the order in Store manager with the NO LABEL selected as the shipping option. Then you can go into UPS.com or USPS.com and create two shipments - one for each box, with the appropriate weights.