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Note that you must start with PIDs that will fly without oscillation.  These PIDs need to be in bank 1 in the following instructions.  Usually the default PIDs are OK, but occasionally they will need to be changed to make them flyable, or to remove oscillations.  If you have or suspect invisible / D term oscillation, set all D terms to zero and multiply all other PID P terms by 0.75 and all other PID I terms by 0.6.

Note that you must reboot the FC after adding AutoTune to the FMS because the AutoTune module is only initialized if it sees it is needed at boot.

The recommended setup for running AutoTune uses a 3 position FMS (Flight Mode Switch).  With this, you can take off and fly Attitude mode with known working PIDs, run AutoTune with known working PIDs and fly Attitude mode with new PIDs, all without using the GCS:
Pos#1 - Attitude mode using bank 1
Pos#2 - AutoTune using bank 1 with SystemIdentSettings.DestinationPidBank set to 3 (that is the default)
Pos#3 - Attitude mode using bank 3 (bank 3 is where the tuned PIDs are written by default)
PID bank 1 should have default PIDs or something that is at least known to fly without oscillations.
PID bank 3 should have default PIDs or something that is at least known to fly without oscillations in case you use it before successfully completing a tune.
This setup can all be done at home, and everything else can be done at the flying field, without using the GCS.
With this FMS setup, you always have Pos#1 to fall back on.  Use Pos#1 to recover from any bad situation or to start over and run AutoTune again.

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If you do enable the AutoTune module manually then it will always be running, even if there is no AutoTune flight mode in your FMS.  In that case your SmoothQuick Accessory knob is always active to change the PIDs in the destination PID bank (default 3) and you can adjust PIDs from smooth to quick any time you want to.

Note that you must reboot the FC after enabling the AutoTune module because the AutoTune module is only initialized if it sees it is needed at boot.

AutoTune data:
The settings used by SmoothQuick are all stored permanently in SystemIdentSettings.  They are Tau, GyroReadTimeAverage, the 3 Beta values, and SmoothQuickValue.  'Complete' must also be True.  SmoothQuickValue is only important if you use the 3x FMS toggle method to select how smooth or quick you want your PIDs.  It stores the current value of the toggle as a number from -1 to +1.

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