I`d look at the damaged area and duplicate it like for like, i`d think the floor of the tray would have a lip folded into it and spot welded to the real wall, if thats the case i`d cut ALL the rust out and replace the rear wall first and then the floor
I can't tell from that pic how bad the back panel is. But to fix the floor I would cut a 2" piece out from one side to the other. Cut a 2.75 inch piece of same length, put a 90 degree bend in it for a lip to weld to the bulkhead, and seam it on. All your welding is then inside so much easier. If the bulkhead behind (or rather underneath) needs attention do that through your newfound access hole
Welding done now,what would be the best to paint over the welds? Also what about the underneath of the truck. It looks like underseal has been used previously