Aldo might be onto something. You select your ship and loadouts, then the mission starts with you departing from your carrier/destroyer and the messages say, if you want to attack from here, proceed to waypoint A. B for another attack method, and c for a third, all of which match up to nav markers. Then, all you need is a series of distance check sexps that trigger a red-alert. The campaign file would then have 3 different versions of the following mission, with the player starting from the different directions on the map in each one, and have red-alert flags for all relevant ships to preserve ship and loadout selection.