I don't know offhand of any source for templates, but I used to make boxes all the time on my old Zund...
I'd take a big sheet of cardboard (tops & bottoms from the boxes my 4x8 sheets of gator came in) and use that... medium scoring wheel first for the fold lines (score/cut the side that will be INSIDE the box), then EOT for the outline. Fold, tape & ship. At one point I was getting all kinds of clever with clamshells, slip-over tops, etc. It's amazing what you can do with a ridiculously expensive machine, a nearly unlimited supply of cardboard, and too much free time. (for that matter, you should see some of the stuff I used to build out of gator scraps!)
I never saved any of those files, since they were always custom-made to whatever we were shipping out on any particular day, but I'll see if I can find a few minutes to bang together a sample file so you can get an idea of how it worked. Really, once you see how it goes, it's easy as hell to make any size/shape you need.
Sadly, I no longer work at that shop, so no more Zund for me, but consider yourself fortunate to have such a wonderful machine at your disposal! They can just do so very much once you start experimenting...
Good luck!