There never is a simple step by step approach to body panel work. The "sandwich" that you are talking about is common, and fixing it is going to depend on severity. You can pick up a replacement support for the inside fairly cheap. Just cut out all of it that is bad and patch it in. For the outside i would just pick up some 16g sheet metal. Once you have the material to patch you can start exploring. Once you find the end of the rust, square up the hole and make a patch that fits well. If the cancer has spread into your raised jeep letters, and you would like to retain them, then it gets more expensive. A licensed jeep replacement panel is much more expensive than a small piece of 16g sheet metal. Also if it has made its way into the floors you can use the 16g to patch it as well.
If you are going to weld everything in, remember to disconnect the battery and clear away all of the bed liner and undercoating from around the area.
And be prepared you could be opening a can of worms.