It's actually easier if you have an AI carrier that's on its own route.
That way, after the first time you load a flight, land on the carrier and save the flight, you can just come back to it and you'll be able to start on the carrier without any bother setting anything up. You may need to edit the FLT file and set SimOnGround to False-- I've read that it's required, but it seems to work either way for me. Just be sure that you don't set it as your default flight, otherwise the carrier will be in a different position. This is because the default flight, by default, is set to use your computer's system time (I believe you can change this, but I'm not sure).
If you're curious, there's a thread at Sim-Outhouse about this as well: http://www.sim-outhouse.com/sohforums/showthread.php?54341-Can-you-start-on-a-carrier