Why are you having to use markers on aluminum moulding?? Are they coming in nicked?
If your saws are cutting properly and you are using the right blades, (fine tooth for non-ferrous metals), you shouldn't have to touch up the miters.
If you are ordering chop and they are coming in with aluminum showing on the miters, I would complain to the moulding company where you ordered them. LJ sends out almost perfect chops on the few metals that I have ordered from them so far. (They are coming out of the Louisiana warehouse).
I don't know what else to tell you about using markers on the surface of the metal mouldings. If they are chipped or scratched, I guess I would either return them or touch them up and let them dry completely before going over them with a cloth, depending on the reasons for the touchup to begin with.