I am currently trying to use FaceTrack NoIR to control a virtual joystick. This virtual joystick outputs axes in 6DOF that I am trying to use to control the view of my cockpit. I believe I have them properly configured in the Options panel but I don't see any roll/pitch/heading movement in the cockpit.

Alternatively, how would I interface FT so that it sends info to LFS?

You can use FaceTrackNoIR's Freetrack/TrackIR output (the default one) with LFS with no problems.

Does LFS automatically intercept that information?

You need to set "Look function" to axis, then it should just receive the information and work. It uses the TrackIR protocol.

You'll need a webcam of course...