I use a piece of cardboard and a paint pen...
Paint one side of one magnet, allow to dry and place cardboard on top of painted side. Slide other magnet over the cardboard until the two magnets are sticking together with the cardboard held in the middle. Paint the top surface of the 'top' magnet.
Put magnets into mod - make sure the painted sides are facing each other and they will be in the right orientation.
The downsides with this method is I can never find my poxy paint pens or I have to rummage through my recycling bin to find just the right type of cardboard (not too thin or it won't provide much cushioning) and my neighbours probably think I'm some mad fecker when they see me rummaging through the bins.
I didn't even know there were Magnet Pole checkers - I'll order one as I can't resist a gadget and the 'where did I put that pen' game gets really boring.