I've got flat magnets that I'm gluing on now. The balls are cool, but I already have flat ones from other games. I'll be using them on 3 ships to get them back on pegs. I just need to ensure I glue the right polarization on right!
Mark the same pole on each magnet with a sharpie or similar.
That is a good suggestion, but it should be pretty easy. I store my ships on the pegs and bases in my Plano, but over the past 3 years, I've had 3 ships come off the pegs. One is a Tie Fighter, another a Tie Bomber, and the last an X-wing. So, I'll just store them with the right pegs and all.
I should mark them just to make sure.
If I were smart, I would've tested the magnets first and all been on the same facing.

