I have never run the tubbie 2's. Just put a set of 3's on the 08 tonight and we will see what that does.
But about your question. I have always used the regular tubbies, and put them as far forward as was reasonable, and flush with the bottom. I like them this way because you get a smooth rail to rail transition (not sure how this would be with the 2's.) And I felt the boat just handled the best with them far forward.
If you do run them flush with the bottom, I would say you need to glass them on, which I have always done. The boats Blowison built for me had them secured with 5200 and screws...but they put them just above the bottom of the hull. They still work very well like this.
Hope that helps a little...