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This version of AutoTune puts the copter into a special version of Attitude flight mode that shakes the copter and measures the motions. As a pilot, you should be able to confidently fly in Attitude mode because it will be a bit more difficult than normal to maintain control. Tuning also needs a larger area than simple hovering in case something goes wrong.
Multicopters fly better if they have "Light Damping (BLHeli)" or "COMP_PWM + MOTOR_BRAKE (SimonK)". Without these, when there is a lot of stick control happening, the copter tends to climb. You may notice this when AutoTune mode starts shaking the copter.
AutoTune is not currently supported on CC3D. Also, there will be a GCS GUI for all this at some time, but it was designed to make it possible to set it up at home and be run at the flying field without requiring use of the GCS.
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SmoothQuickSource:
There is a virtual slider called SmoothQuick, and the PIDs you get are in the middle of the slider. At one end is smooth which may be preferred for photography. At the other end is quick which may be preferred for racing. Once you have run the tuning, the FC will remember the tuning and allow you to change PIDs along this sliding scale at any time in the future (as long as you don't start the AutoTune process by staying in AutoTune mode for over 2 seconds while armed, even if you do accidentally start an unwanted new tuning you can just power it off without disarming to forget the new tuning before making it permanent). SystemIdentSettings -> SmoothQuickSource is where you configure how to adjust the slider (it is not where you adjust it). SmoothQuickSource = 0 disables this entirely. The default of 25 says to access the next of 5 points on the slider by toggling the Flight Mode Switch (starting outside of AutoTune) into AutoTune and back out, 3 times (less than 2 seconds), but only if armed. If you think of the slider as a scale from 0 to 100, with smoothest being 0 and quickest being 100, then you start out at 50. The first time you do the fast FMS 3x toggle it will move you to 75 on the slider, then 100, then 0, then 25, then back to 50, etc. So while you are flying the new PIDs, you can adjust them in real time. If you do the fast FMS 3x toggle while disarmed, it will always set it to 50. You can also set SmoothQuickSource to be a number from 10 to 13 which corresponds to using Accessory0 to Accessory3 to directly adjust the slider, in real time, while you are flying the tuned PID bank. The settings needed to be able to set PIDs this way are all in SystemIdentSettings. They are Tau and the 3 Beta values. 'Complete' must also be True. You can copy these from another FC or from a previous tuning session and 'export' your PIDs with SmoothQuick.
AutoTune tries to produce results that to make the tuning flight correctly tuned. That does not take into account the non-linearity of thrust response. To remove high thrust oscillations (or increase stability during descent), use TPS to decrease PIDs at high thrust (and if necessary, increase PIDs at low thrust). Typically you want the TPS curve/line to cross the horizontal axis at the point (thrust value) where the copter hovers. Examine SystemIdentState -> HoverThrottle after tuning and before you power off (not saved) to see what your hover thrust is. Beware of throttle bloom that happens when slow responding ESC's make a copter climb just because of the fast RPY controls.