I noticed a big improvement in the precision of the tracking when I changed from the passive-reflector TrackClip to the active-LED TrackClipPro. I seem to have far less "crosstalk" between the axes now. External lights and reflections have less impact. And with the simple clip, my TrackIR often lost its mind and had me staring either straight up or straight down.
As for the profile, I'm lazy. I use a copy of the default, with all 6 axes enabled. I do, however, have both the TrackIR "center" and "pause" commands mapped to buttons on my CH Throttle. I often pause and re-center just before firing. In concert with the AH view zoom control I have mapped to a hat switch on my CH Fighterstick, it models my moving my eye up close to the gunsight.
YMMV
(As much as I love my TrackIR, I plan to move to an Oculus Rift as soon as I can.)