ORIGINAL: guver
Should I start out with both sides perfectly level with wings (in center) OR perhaps center the left on and make the right one a few clicks UP?
When might one leave them both below center of wing (that is both down) OR would they both ever be UP?
In regards to that first question above: Yes in initial setups always set up both ailerons in trail (trailing edges lined up with the trailing edges of the wing. I prefer to do this by standing to the rear and lining them up visually. I beleve this method works better than even the straight edge method on the bottom of the aileron since some airfoils that is not as effective. It also works well in cases where there may be some twist in the ailerons.
In regards to your second question above: rigging in neutral some flap (both down) or some up also called reflex or spoiler (both up) is not normally done in initial set ups. Both are sometimes used to effect some changes. For example both can be used for sometimes used in small doses to affect the airplanes approach characteristics. Flaps can be used to slightly aid in slowing the approach therefore increasing the angle of the descent. Spoiler can be used also be used to slightly increase the angle of descent without slowing the approach speed.
In regards to twisted ailerons out of the box. This is very common on many arfs do in part due to their increditable journey and climatic changes from the factory to our local flying fields.
Now always the best answer is to fix them by counter twisting and reheating with an iron and so on but since this occurs on about half the airplanes I inspect the simple solution especially when at the field with a new trainer is this technique:
Lets say the just one aileron is twisted and not the other (either side) then simply rig the straight one in trail and the othe stand back and look to eyeball. Split the difference, make it about equal at the root and at the tip no matter which way the twist.
Now this of course is not rocket science but then agine nothing we really much do is. Its an effective expediant that works just fine.
John