Hi,
The manual shipping method has no setting for the weight of the box: its weight restrictions are compared with the weight of the products in the cart. But you can have the box included in the weight of each product automatically with a mass action:
1. In Display > Custom fields, create two custom fields for the table "product", for example "Net weight" (column name net_weight) and "Box weight" (column name box_weight). Enter both in the same unit as the weight of the product.
2. In System > Mass actions, create a mass action on products with the triggers "After a product is created" and "After a product is updated".
3. Add the action "Update the values", select the column product_weight, choose "A calculation" and enter:
product.net_weight + product.box_weight
Then, each time you save a product, its weight becomes the net weight plus the box weight, and the weight restrictions of your shipping methods use that weight.
Note that the weight of a product is multiplied by the quantity in the cart, so this works well if each product is shipped in its own box. If several products are shipped together in one box, the box would be counted once per product.