Depends on the size of the magnet. But the best tools I've found for the job are a drill bit the same size as the magnet, plastic tweezers (hands down the best purchase to have when using magnets), and plenty of patience. Put a dollop of paint where you want the magnet to go and while it's still wet place the second part where it would be glued...voila...the paint will transfer to the other piece giving you a guide as to where you should be drilling both pieces.
***we could probably move this to the hobby section as it really is a good guide for any game***
