I struggling with accurate placed and geometricly true as well.
I don't know what size of holes you do, but I imagine small. It makes a difference. I usually work bigger than about 1 mm. Most often between 3 to 12 mm.
I had a lot of trouble popping the centre mark and then getting the hole there. I only work either markking and I read no dials, or marks first hole and then there are only permanet marker crosses to eliminate complete mistakes if I use dials.
1) Drawing the line. I found out that I'm better off scribing the lines straight and holding the scriber straight, note that this will require some off set from the rule, if you are using it. Canted scribe line does not "crab" the punch to correct location. Something to do with the burr or something, hard to imagine that slighty inclined groove would send it on the other side.
2) Popping the mark on the right place: a) Use small sharp 60 decree to get the punch on the right place. b) Locating the intersection: I'll draw the punch on the line until I'll feel the "intersection", you probably want to draw the line you draw last, othervice you'll bump the "wall" of the other line. c) Punch absolutelu upright and LIGHT tap to get very small pip.
3) Inspection: mark can be driven with a gentle taps close the final location. If driven or uneven burr, I always file the surface smooth, the uneven wall will play havoc
4) If the hole is large I finaly pop centre with larger 90 decree punch and check it again
5) I aim that punch visually, larger drills will pull light objects centre, when gently touched with a drill, but wiggler works also for me.
6) I have found that using spotting drills will put the hole exactly where aimed. Pop rivet drills come close second, but I have no luck with normal drills, they wander all over. There are many different types of drills, many will drill happily after they have good centre to start, but on thin drills only spotting drills seem to get the start right (I use 3 mm quite often).
Sometimes I'll locate first hole with a wiggler and then work from there a dial indicator, works only a very small distance, but with very good accuracy.
Biggest improvements I had was to learn to make the punch right, most of the time I'll file the "crater" even and the correct drill will make or break it.
I'm not sure if this helps, but when I drilled PC boards and such, learnt little about drils.
Pekka