Attach each alligator clip to a flat headed nail by crimping, soldering, or both (soldering works best). Once soldered, magnetically attach one of the stick magnets to the flat headed nail. Now build a little pyramid base using the ball and stick magnets. Finally, attach the alligator clip stick magnet to the ball at the top of the pyramid. Voila, holding tool.
These little magnets are super strong, so the holding tool works well. If you need a heavier base, just add balls and sticks to the base of the pyramid.