The single most important thing IMO is, if things aren't working the way you like it, keep tweaking it until they do. If something's bugging you, it's likely to keep bugging you until you fix it.
Try to find a profile that works close to how you want it to, and tweak from there. Fugitive had a post with a big bunch of profiles for download but for some reason I can't find it the last couple days.
TrackIR's settings are the single most personal setting in the game IMO. Way more individual than joystick settings. The time spent tweaking is well worth it.
Myself, I use a very aggressive profile for moving around the cockpit but for the most part only use side to side movement in actual use. About the only thing I can't get a decent six view in is an F6F and to a lesser extent, the P47D11. Everything else I can see out the back fine.
Wiley.