Grits, all you have to do is copy and paste your stick setup into AH2 and you'll have no problems with AH2 seeing all 3 of the CM devices.
GoFaster, I'd recommend you don't use the joystick trim and actually use the AH based trim keys. If you use the joystick trim you will lose airspeed, minimal airspeed, but even a little bit of E can save your life. Not to mention you can rip wings at high speed in some aircraft if you even nudge the trim tabs.
Waffle, I'm not sure you have the prothrottle, but its better to have your view there to keep your stick hand doing as little work as possible (least imho). You want to also use the sliders to dampen the stick a little, its a bit too responsive otherwise.