Homebrew PCBs

What I've been doing is including a "target" in my prints (four 25 mil
squares in a square, with a 1 mil gap - that translates to a 1 mil ink
crosshair when I print negatives).  I print this on all photomasks and
one on plain paper.  The plain paper one I use to pre-drill 16 mil
holes at each crosshair.  Then, when exposing, I can line up the holes
with the crosshairs pretty accurately, and double-check through the
glass overlay.