Hmmmm, if I understand correctly, the idea is to split the BOE into tiny chunks to make it manageable.
You couldn't conceivably have all 30 cap ships that will take part in the battle all slugging away at once (as awesome as that would be).
Splitting the missions allows for parts like, "Take down StarDestroyer X with support from Frigates A and B," and once that was done move to, "protect transports C through G from Interceptors Y for 10 minutes," without having X, Y, and A through G all in the same map.
Hope that was clear and accurate enough.
How about instead of half-a-dozen red alerts, you have one or two red alerts followed by an end mission. This could simulate returning to the carrier for warheads, fuel, repairs, etc. and could handily explain how you get a shiny new fully armed fighter two or three times during the battle.
Just ignore the fact that the battle probably passed too fast, and that the Rebellion didn't have sufficient rescources for that sort of thing.