This is just a theory, I haven't fully tried it out yet.
Placing the carrier (with AICarriers) and then being unable to film a landing on it because it's moved and FS Recorder can't record it has led to many solutions often hinging around programming a route for an AI carrier.
There's one thing I haven't heard of being tried yet though, and theoretically a bit simpler. With FS Recorder you have the ability to record a flight and then play it back as traffic. The idea being you can record an new flight and fly along in formation with the flight that is playing back as traffic. If you record the new flight also, you can build up a formation of several layers.
Nothing new there, except that Bruce Fitzgerald has made a pilotable version of Javier's carrier. This means the carrier behaves like a user aircraft (well you know what I mean). This should therefore mean that you can record it with FS Recorder and play it back as traffic....and it will show up exactly where you expect it to be even if it's moving. Then fly an F-18, record this flight too, and land on the carrier. Save it all then ready-up Fraps and film the final playback.
I've certainly managed to "fly" the pilotable carrier, record it, play the recording back in FS Recorder "as traffic", fly an F18 and land on the carrier. So that bit works. If I also recorded the F18 landing, that should yield a playback that includes both Carrier and F18, and both in the right place at the right time for filming with Fraps. At least that's the theory...haven't tried the final step yet.
(The pilotable carrier seems to have a very unstable deck once you land on it, so it seems to be no good for cat launches.)