Actually, if you are using our standard USPS.com rate lookups, you should configure your container types with the Weight of just the empty box itself (including any extra padding/packing material that would normally go with it).
Then you would configure each product with the Weight of each unit of that product (including any extra packing/padding that would get wrapped around each unit), choose which type of packing container it ships in, and how many units of that product would fit into that container type.
The container names are just a convenience to help you keep track of which container is which; regardless of container type, they all get looked up with the Postal Service using their "package" rate (we compare First Class vs. Priority Mail and apply whichever is cheaper). If you have more than 3 sizes of box and no actual "envelopes", you can just use our "envelope" container types to define additional boxes.
Products configured to ship in the same container type can share containers (e.g., an order for two items both configured to ship in a Small Box with a packing capacity of 2 would calculate shipping with the weight of only 1 Small Box added to the item weights).
Tubes are a bit special, as they can also consolidate from smaller to larger tubes (e.g., an order for one item configured to ship in a Large Tube with a packing capacity of 2, plus another item configured to ship in a Small Tube, would calculate shipping with the weight of only 1 Large Tube added to the item weights).