Arduplane setup question

I am setting up a plane I have been flying in manual mode.

My question is, how do I do the transmitter calibration ? The docs says to trim the center points before calibration. But what about end-points ?

Should I calibrate with the same settings used for manual mode without flight controller ?

That is -80..80 on rudder, -70..0 for flaps etc ? Or should I calibrate with full range on transmitter, and only worry about center trim ?

Let us assume in manual mode, I have limited Tx to send 1200..1800 as that is the max amount of servo travel I want.

I am a bit insecure, because the APM could decide to map input 1200..1800 into 1000-2000 on the outputs, or it could keep it (in non-manual modes).

What is the autopilot limits on output ? 1000-2000 ? or the 1200..1800 I am using in manual mode due to end-point-adjustment ?

My best guess is to use the same Tx profile for both manual and flight controller mode, and thus calibrate with limited range after EPA. 

Documentation should be updated for a beginner like me.

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