A lot of times, I would just cut the pieces off after I'm done with putting the rest of the pieces together, and put the cut off piece aside to modify it. I also usually use the scrap pieces of the borders on the printed paper and cardboard to make shapes.
I highly encourage using cardboard scaffolding in your weapons btw, closed peps usually warp in one way or another during either resining or rondo stages.
As for the zoom function, you can calculate just how large you need the piece to actually be, put together the original, put together the new larger (or smaller) piece separately, and finally put the new piece on the original.
If you're looking for a literal "zoom" function on pep designer 3, you're out of luck.