Each of the fighters will create a separate salvo, so you'll be fine.
Say you have a ship that will take two missile hits before goin' boom. If you have ten salvos of two missiles, only one salvo would be "used" to kill the ship and you'd have nine salvos remaining (Assuming they had sensors). If you were to fire a single salvo of twenty, however, every missile would hit the small ship.
A salvo, as defined by the game, consists of all missiles fired from a particular fire control on a specific ship (And perhaps based on missile type: If two missiles have different speeds, it won't matter if they were fired from the same FC). So, a ship with eight missile launchers evenly distributed between two fire controls will launch two salvos of four missiles.