Yes, you need to seperate the axle clamp from the inner tube so that the inner tube may be slid past the bearings and seals.
In my opinion this is the only difficult part of a rebuild. the axle clamp is attached to the inner tube with
90 foot pounds of tourqe and lock tite.
If you let the inner tube slip in the vise, or you do not use soft jaws that grab around the inner tube you may dammage the inner tube. If the inner tube gets damaged the seals will probably be torn by the damaged inner tube. If you make the inner tube out of round the seal will not seal properly.
Use the proper clamp for the inner tube and you should have no problems.
Check this site for more pictures
http://www.garagegirls.tv/album/forks/