Welcome aboard Andy!
I looked very closely at the carrier thing and mentioned it a while ago. Unfortunately you can't do it.
I have a file which I haven't uploaded with carriers in groups of 3 in various regions of the world. I wanted to have them landable and also have AI (F15s for example) flying between them 24 hrs a day and doing circuits. Great fun fitting into the patterns to land and take off yourself!
However, for it to work you'd have to have an 'airport' on each one with taxiways, parking etc for the AI to work. You can do everything I found and I got an AI Cessna doing circuits from a carrier.
EXCEPT only one problem.
As soon as you connect up the parking and runways because of a quirk in the way FS9 now stitches the scenery levels together, something weird happens as you can see from these pics.
The sea climbs up the sides of the carrier. It's not the carrier that's the problem - check out Meigs and you'll see the sea does exactly the same there. It's a fault in the FS9 scenery system which I think either M$ didn't notice or they hoped people wouldn't either notice or care about.
I think I was the first to notice it and I've raised it on the 'pro' scenery forums but so far no results.
It's a pity because I have the carriers appearing in the airport list with navaids making them fully flyable. By fiddling the FDE of some fast jets it wouldn't be difficult to make them land and take off from the decks - but there ya go.
Maybe if M$ can solve the levels problem......