If you want to fly from carriers in single missions, this is what I did:
1. Go to the download section (maps / terrain mods - environmental mods) and download the water_maps_1.02 by Kodiak http://combatace.com/files/file/12804-water-maps-102zip/ and follow he instructions to place the water maps in each terrain folder.
2. You need to ensure that the plane has the following statement in its data.ini: CarrierBased=TRUE. If it is obviously a carrier plane, it will have this statement.
3. You need to ensure that the plane has a carrier available in the Groundobjects folder from its respective country with corresponding service dates. If it's USN this will not be an issue.
4. You need to ensure (as Kodiak made clear) that the following statements are in the terrain.ini of each map you plan to fly from:
Example for VietnamSEA:
NavalMap=TRUE
WaterMap=VietnamSEA_Water.bmp
It should work now. This all assumes you use the mod folder and have extracted files from at least the terrains you would like to use. If you haven't, then you will need to set up carrier missions using the mission editor as already mentioned.
I hope this works for you.