The Equipped checkbox doesn't change the weight carried however. It's more for making sure you are wearing the armor, or shield or magic item that is granting you a bonus or penalty. There are some options. Probably the easiest is to edit the weight. If the item is a 3 lb sword, edit the "3" to say "b3". (for Bag of Holding, 3 lbs). The entry is no longer a number and will not be added to the weight. This doesn't allow you to calculate the amount of weight the bag is holding, though, if it's too much to eyeball. The best solution I know of for that is a second dedicated character sheet called, "Bag of Holding", that has all of the inventory of the bag.