1) You can do either or. The only benefit of doing it in game is being able to record TrackIR movements not recorded in AH films. Otherwise, AH Film viewer won't interfer w/ your flying (mainly a hit on your FPS while in game).
2) Click on the "Movies" Tab and in the Video Capture Hotkey box, click in that box, and then hit a key you want to use to record. I believe F12 is default. But I use keys less likely to interfer with the AH game/Film Viewer when i push record. I.e. I hit X key and it records my fraps movies and sets autopilot. Personally, I use "9" key.