Here is a few tips to get good centering of vias & through holes.
1) Copy and paste your final PCB layout to the desktop & rename "xxx Shrink",(where xxx is your own board name)
2) Open your renamed copy & reduce all of the hole sizes to 0mm5 (0.5mm). Save and close.
3) Use the renamed copy as your master, Print & expose in whatever method you using(U.V. Toner Transfer etc)
4) Etch, clean & electroless plate(if used)
5) Use a spring loaded center-punch(google Automatic center-punch) on its lowest possible setting to "dimple" each hole & finally drill with a 0mm8(0.8mm) drill bit. Take your time with this step to achive precise holes!
6) Enlarge any other holes to their required diameters
Using this method takes longer but stops "run out" ,wandering & fewer bits snapping....AND gives you a near perfectly centered hole when using a Dremmel Drill & Stand
I hope this helps with tha alaignment problem on S/S double & D/S Boards
Chester