You have your runways and planes, now you want to know the best set up for your attack phases. I will recommend some tactics you can use for your own fleet. All my examples are for carriers level fourish- six. If you are a VIP carrier, this kinda won't help you. VIP are a different story. Ship level costs.
Tactic one, Anti-Carrier setup.
Your first wave should include fighters and torpedo bombers with some dive bomber support. You should have at least 15+ fighters with at minimum 5 runways. The amount of dive and torpedo bombers are your choice.
Wave two. This wave should be staggered or should be about 6 or more seconds after your first wave. The first planes to launch should be one small wave of fighters, about the same as your runways. After that, you can put down some torpedo bombers or dive bombers. After that, place the same amount of fighters as runways. The objective of the first wave is to destroy all fighters/ AA your enemy has. If there are still fighters, launch all of your second wave fighters, then wait until the enemy fighters are dispatched then launch your bombers.
Wave three. This isn't required but helps out for destroying things that aren't carriers. This wave should be five seconds afters the last plane you launch from wave two. This wave should focus greatly on bombers, with little to or no fighters. By now your enemy should be crippled, so torpedo bombers are best to finish the job.
Notes: As for ship tactics, you should back off or run away if fighting ships. If fighting carriers, back off, or stay and shoot his fighters down if you have any fast firing cannons. I say fighters as once their fighters are down, your fighters will destroy their bombers. If the third wave doesn't destroy or sink their ship, keep launching your planes after they've returned.
Tactic two, Ship Killer setup.
Wave one. A small force of some fighters, with a lot of dive bombers. The main focus is to cripple their speed and their AA guns. Dive bombers are best for crippling their speed compared to torpedo bombers due to the torpedo's accuracy against fast small ships.
Wave two. Like the other tactic, stagger the launches of each wave. This is the wave that should cripple them even further or completely destroy them. This wave should have nothing but torpedo bombers and dive bombers.
Notes: If you face a carrier, back off. Wait until they can't support their fighters, then snipe with your fast firing cannons. You don't have a huge fighter force like tactic one, but once their fighters are gone, you can snipe the carrier. Ship tactics, back off while launching planes as one hit on your flight deck could take out a good chunk of your attack force. If you're doing this tactic, it's best to have a good amount of toughness and firepower.
Tactic three, Battleship Support?
This is an unusual one. It involves you making the carrier deck and runways on the stern or back of your battleship. When making this one, you should have one wave and just one wave. It very important to have only one wave due to the fact you want your guns to be firing as soon as their ready. As for plane setup, mostly fighters as if you face carriers, you need to have the fighters to shoot down their bombers. Having a few bombers can be handy as if you face a fast moving boat your dive bombers may hit and heavily cripple their speed.
Notes: This tactic allows battleships to distract their enemy. If your fighting another battleship, the planes can distract them. A cruel tactic is to have some torpedo bombers mix in with the fighters. As they both fly at the same height and can be hard to differ, especially when fighting another ship. You don't need many bombers as your guns will do or replace their job.
Edit: You'll need to elevate the runways and flight decks so your superstructure doesn't block the runway.