I have a 9C radio and understand about geometry and resolution on a servo pretty well I think. But for starters, the 9C has all default end points set at 100% which looks like it gives my servos about a 45* swing. Should I drive my end points to 140% to start, then set my high rates say for the elevator, so I get a 45* deflection with the geometry of the servo arm and elevator horn? Or should I back off on the end points to a lesser number then set my high rate throw with the arms?

I would suggest that you set up your high rates at 100% attempting to use geometry of the linkages to attain desired throws and then use the computer to make up for mechanical deficiencies that just can't be otherwise worked out. Then set low rates wherever you choose at a point below that.

You really don't get much more throw with those last few degrees of servo wheel turn if you really study it closely. Most of your throw per degree of rotation is near the neutral point.

Most servos give you a 60* travel. Set your control surfaces up to give the recomended travel using100% as your default. Do this by varying the distance from the clevis to the hinge point. Then you can us the ATV option on your radio to fine tune travel.
As Bruce88123 mentioned, the further your servo wheel travels from center the less linear travel you produce.

Ok thanks, now from what I have read, people are saying never run your ATV above 120% or below 80% and never run your low rates below 50%. Now that I think I have the high rate thing figured out, how would you not run your low rates below 80% or even 50% if your low rate surface deflection is only about a 3/8" deflection? I am dialing my dual rate all the way down to around 25% or 30% to get a small low rate deflection. Am I doing something wrong? At zero subtrim, and 120% ATV with the servo deflected to a 45* throw, the high end looks good, but I feel I am loosing too much resolution on the low end.