"Except for the hot-loaded planes, all armament aboard Tarawa was stored in blast-proof lockers beneath the flight deck, only to be hoisted out and loaded on just before launch." End Run, p.167_
It's a little rough, but I've got an idea for that. A section of deck plate raises to reveal groups of blast-proof lockers. Each locker has its own set of missiles. Should a group of lockers become empty or not have the type of ordinance required, the user can lower the first group and raise another. The neat thing about this specific system is that when all is squared away, I just have to draw red and yellow lines on the deck.
I toyed with the notion of having dispersed lockers all around the flight deck, but after playing around with some fighter silouhettes, I got the impression that half the time some plane or other piece of hardware would be parked over the hatch.