Step 1: Sources for materials
Tools: A pair of tweezers or forceps for picking up the crystals (if you can find plastic ones, these would be better than metal), and a toothpick for repositioning.
Step 2: Attaching decorations to magnets
Pick up one of the crystals with the forceps and place it on the glue. You'll find that if your tweezers are made of metal, they will glom onto the stack of magnets, possibly causing you to drop the crystal, which is why plastic ones would be better. An alternative is to place a crystal facedown on a surface and then dab the glue-covered magnet onto it.
Since superglue sets very quickly (duh!), you have only a few seconds to reposition it by pushing it around with the toothpick. Allow the glue to dry for a few minutes.