If you are installing on foundation, I would think you would put the package
into a single box (medium or deep). Then add each additional box of
foundation after the ones already on have been drawn out.

As for the tube entrance, That should work regardless of the size of the
hive body used. Any wire mesh used at the bottom to close off the entrance
or for a mesh floor would have to be quite small to keep out the hive
beetle, since it is about 1/4 the size of a bee (or less).