Its pretty easy actually, you just need to get the right size magnets and a bit to drill the holes in with. For your normal troop size (Like Fire Warriors or Space Marines) I used 1/16 x 1/32, I buy them in bulk from this guy:
http://www.ebay.com/itm/281794706969?_trksid=p2057872.m2749.l2649&ssPageName=STRK:MEBIDX:IT
As for the polarity, that is easy to get right. The first thing I did was drill a hole where the head went in a body and placed a magnet inside. After that, I placed a stack of magnets on the end of it. I then took a head and drilled a hole in the bottom. Then I took the body with the stack of magnets and used it to push the magnet on top of the stack into the head. I usually do not even need glue for this, if the hole is deep enough, it should be snug enough to hold on to the magnet. Doing it this way ensures you have the correct polarity everytime. I did all the heads next this way, and after I finished here I took the magnet stack and placed it on the end of one of the heads. This btw, looks metal as fuck because it looks like the head has a metal spinal column sticking out. Then I drill a hole in the rest of the bodies and use the head to place magnets into the remaining bodies. The arms are done using the same magnet, I like to make sure that the arms and heads all have the same polarity, so when I am bored I can piece together some abominations.
If you need, I can take pictures tonight after work.
Also, I got some more kits.