I just helped a friend "stack" his truck last Saturday. Cut the old stuff off, cut a hole in the bed, weld (or clamp) the new stuff together, and you've got stacks. Not difficult at all, just time consuming. Make SURE you measure for that hole in the bed twice...
Another option is to run the stacks completely outside the bed, right behind the cab. I personally don't like this look as much, but if you need your entire bed, it'll let you run stacks without losing any bed space.
Keep us posted on what you end up doing!
Dave