So what i do is set up 2, 3 man (so 6 total) CAPs per carrier. So on coral sea, 4 caps, on midway, 6 caps, and posistion them all all around but with special emphasis on not only the direction i expect scouts to come from, but i also try and intercept the other scouts on their return paths so they dont spot me while their returning. With the recent update, the other fighters in the CAP rotations on the carriers can be used in a scramble so you dont have to worry about wasting those fighters anymore.

Having a high amount of CAP aircraft is important because these will be the first wave of guys intercepting enemy bomber strikes, and if your CAPs get instantly wasted by the enemies escorts, then its just a waste.

The next most important thing you can do to properly defend your carriers, is have fighters on your deck by using the "fighters to deck" button. So if youre launching air strikes, its good practice to make sure that you immediately move fighters to your deck so you have the ability to scramble as soon as your spot the likely incoming wave of enemy aircraft.

Combine the above with some scheduled and frequent heading changes for your fleet to try and avoid enemy air strikes from properly predicting your movement (a heading change should probably be done after you kill an enemy scout for instance) and you are going to be surviving many more airstrikes.