What if you assaign certain fighter/bomber wings to certain carriers ahead of time. You would use your fleet points to deploy your fighters from that carrier, after which, they would operate as they do currently, untill you commanded them to land again.
However, at the end of the battle, you would have to scrap any fighters that do not have a carrier to land on (probably because it was destroyed or captured during the fighting), as they did in WWII. You would choose what to get rid of, of course.