I haven't tried gluing things, yet, I use mini binder clips to hold things together.
I already line up a set of holes with the last set by putting a tone in the last hole of the previous set.
I do prefer to mark my stitch spacing with a wheel and poke holes as I go. But, for an upcoming project where I need to pre punch holes, and find them easily, I think the chisels will be better. I think I will punch each piece separately. As my patterns are all based off a common center line I think I will mark that center point on the bottom edge of each piece and work out from there, alternating sides for each punch, rather than around from an end. If I start with a tine on the center mark and the rest to the right, I'll punch my next set of holes to the left, starting with one tine in the hole at the center line, and repeat alternating sides. This should give me an equal amount of holes all the way around, and be repeatable on each piece.