I keep the mags in different boxes (separated by caliber and capacity). When I go to the range I separate them in my bag and only shoot one gun type at a time. Realistically for range purposes it's probably fine (I've shot 9mm from .40 mags and vice versa), provided the mags aren't pre-loaded with ammo.

For carry purposes of course check and recheck, just like you'd regularly check your carry ammo.