Take your newly cleaned and dried coins and pick out the ones you want to magnetize.
After picking out the coins, be sure to set the coins with the side you want to see facing down. It would suck to accidentally glue the magnet to the good-looking side.
Take your bottle of glue (or other chosen adhesive) and put just a small amount on the back of the coin. Too much and you'll just waste and make a mess. I found that a small drop works the best (see the second picture). You want just enough to fill in the surface underneath the magnet and have a little ridge around the magnet.
Take the magnet and slowly push down onto the coin. Make sure the magnet stays centered on the back of the coin. Once you've put the magnet on there, move on to the next coin.
Personally, I haven't had a problem with the glue I used yet. The magnets have been in use on the fridge for about 4 months now, and I haven't lost any coins yet. The only possible change I might make next time is to rough up the glued edge of the magnet (if possible) to help make the bond to the coin stronger.