Craft stores typically have some nice multi-compartment containers designed for beading (I think). I picked up some nice containers from Michaels, but probably any craft store would have them. I used those for a while, but lately I've just been using cheap Glad leftover containers you can get from Target or any grocery store. Here's the reason ... once you get your axles prepped and clean - and especially after you put on the jig - you'll want to store your axles upright. So take any old junk block, cut it down to a useful size and drill 4 holes in it to place the axles. I put everything for one car (wheels, and axles upright in block) in the a Glad container and seal it with the cover.
That works for me. I'm sure there are dozens of good ways, but the key is to be able to hold the axles upright and seal everything away from all the floating balsa dust as you toil away sanding yet another set of fenders.