paints his favorite from 
Meanwhile, I had ordered some magnets from K&J Magnetics, to match the width of the holes and the thickness of the acrylic.
I had some vague homes that I would just push the magnets into the holes and everything would fit... but I found that it look some force to do that, and the acrylic would often crack and sometimes break into pieces...
So I got out my ratrail file - which happens to be about the same diameter as the holes - and filed the holes very slightly. (Too much, and the magnets fall out!)
If you want the bases to stack nicely, then you'll need to make sure the magnets are "going the same direction" polarity-wise. For your first base, mark the magnets with a Sharpie marker as you take them from the stack, then make sure the "black" ends all face the same way on your base. For later bases, just place the new magnets on top of your old base, then press the new base onto the old base!
Another key to not breaking the acrylic bases is to apply pressure straight down over the magnet, not to the sides of the magnet.
There! It's not that hard.