You can do either beehappy. I converted all my deeps to mediums by cutting the excess off the bottom of the boxes. From there I was given a bunch of extra wood, so I turned all of them into shims, and cut a notch out of them and they make handy upper entrances.
Personally I don't like drilling holes in the bodies, but I know others that do, and it requires less equipment and less money. Both work just fine.