Recommendations for mapping X56 Throttle and Trim controls

I recently upgraded from a basic 3-button+POV 4-axis joystick to the Saitek X56 6-axis joystick + throttle combo. In addition to many more buttons, it's a dual throttle and also includes 3 knobs. As I find using the keyboard too awkward an interface for many controls, especially maintaining trim controls, I'm hoping to move them to the X56 Throttle. Previously, I'd normally not even bother trimming putting a lot more strain on my joystick hand, at least until I activate the autopilot. However, I'm finding the interface less than optimal.

The two main items, map trim controls in a reasonable fashion, and map the throttle axes as well.

The X56 Throttle has two horizontal analog knobs on the right side of the throttle. It seems very natural to map these to aileron and rudder trims. Especially having that center detent, it would be easy to verify that they are reset to sane default before take-off. I would also expect that the auto-pilot to keep these close to center during a straight and level flight so the hand-off shouldn't cause too much of a jump. The knob on the left is mounted vertically which makes sense for the elevator trim and it's actually a digital knob so it's akin to up/down buttons with a detent for each press. This also seems to work well with the auto-pilot as I'd want to retain the same elevator trim setting. However, when I went to map them in FSX, I found that only elevator trim was available as an axis mapping and the aileron/rudder trims were only mappable to buttons/keys. Is this really a hard limitation of FSX or am I missing something?

Well, I decided to then just swap my choice for aileron and elevator trims and ignore the rudder trim. I found the nice, smooth (except for detent) analog control works wells for the elevator. At some point, I set the autopilot and let it run for a while. Over time, it moved the elevator trim down quite a bit (I think I still had it set for my initial climb out.) 20 minutes into the flight, all of the sudden it jumped and I started climbing while the autopilot tried to regain control and resume my altitude hold level I had it set to. As best as hI can figure, what happened was my fancy 10-bit resolution analog elevator trim changed by one point causing the trim to instantly jump to the last value I had it set to from the knob. Even though the autopilot was on, any change in the analog knob takes precedence causing it to instantly jump to the absolute position of the control. Since having the autopilot physically change my knob is out of the question, I think that there are only 3 options: manually make sure I keep my elevator trim close to what the autopilot wants, disable my trim axis somehow while autopilot is on, or move it to the digital know and forget about trimming aileron or rudder. As for having the aileron/rudder trims somehow mapped to an analog knob, I think that would only cause a significant problem if a jump happened sometime while the autopilot was turning.

The other issue, the dual throttle on the X56. I mapped the left/right throttles to throttle 1 and 2 in FSX. While it doesn't benefit my flying single engine aircraft, I can experiment with it on the Learjet 45. Last night, however, I discovered a bigger problem with that mapping. When flying a 4-engine aircraft like the 747, I only end up engaging the left two engines making any kind of flight pretty might impossible. I have to remap it to master throttle and nothing whenever I switch to 4-engine aircraft. As far as I can tell, there's no method to map the throttles in pairs to support only two axis of control. Is there any method to have mapping change automatically for specific aircraft?

And lastly, even with a 2-engine Learjet, one thing I loose is the ability to due reverse thrust. How is this normally handled with USB throttles? From what I can tell, there's no way to make my physical throttle control go negative, and if there was, there's no detent to find zero. Also, if the throttle is bumped at all, it might reset the reverse thrust back to zero if I push it negative from the keyboard.

Any suggestions on how I can better improve my control mappings to best accommodate FSX?