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SystemIdent stabilization mode:
AutoTune is a flight mode that can directly go on the FMS.  SystemIdent is a stabilization mode that can be put in a Stabilized1-6 flight mode.  There is no reason to use SystemIdent stabilization mode.  What you will get is a mode that acts a lot like the shaking part of AutoTune, but the shakes may be bigger or smaller.

Field descriptions:
System.SystemIdentSettings are stored permanently but do not show up in logs.  DataObjects.SystemIdentState shows up in logs but is not stored permanently.  Read the source if you need to know more of the technical aspects of these their fields.
- Tau, Beta (3 values), and Complete are the only fields used by SmoothQuick.
- DampMin, DampRate, DampMax affect the control damping.  Decrease damping to make your aircraft response more rapidly.
- NoiseMin, NoiseRate, NoiseMax affect control sensitivity.  Increasing noise (sensitivity) will make your aircraft respond more rapidly, but will cause twitches due to noise.
- Damp and Noise put together form the dual virtual slider SmoothQuick
- CalculateYaw can be False,TrueLimitToRatio,TrueIgnoreLimit default is TrueLimitToRatio
- YawToRollPitchPIDRatioMin is enabled with CalculateYaw default is 1.0
- YawToRollPitchPIDRatioMax is enabled with CalculateYaw default is 2.5
- DestinationPidBank default is 2
- TuningDuration is 60 seconds
- SmoothQuickSource default is 25
- DisableSanityChecks disables certain checks that stop the PIDs from being written default is false
- Complete is set true after a successful AutoTune run.  It must be true for PIDs to be written to DestinationPidBank  

System.SystemIdentSettings:
- Is stored permanently
- Is not logged
- Is reset to default values if you stay in AutoTune mode until the shaking starts (about 2.5 seconds).  As with other data changes, this is not stored permanently until you disarm.  If you power off without disarming, the reset values are not stored permanently.
- Tau, Beta (3 values), and Complete are the only fields filled in by AutoTune.  Other fields are used by SmoothQuick to convert Tau and the Betas into PIDs and check and limit the PIDs.
- DampMin, DampRate, DampMax affect the control damping.  Decrease damping to make your aircraft response more rapidly.
- NoiseMin, NoiseRate, NoiseMax affect control sensitivity.  Increasing noise (sensitivity) will make your aircraft respond more rapidly, but will cause twitches due to noise.
- Damp and Noise put together form the dual virtual slider SmoothQuick
- CalculateYaw can be False,TrueLimitToRatio,TrueIgnoreLimit default is TrueLimitToRatio
- YawToRollPitchPIDRatioMin is enabled with CalculateYaw default is 1.0
- YawToRollPitchPIDRatioMax is enabled with CalculateYaw default is 2.5
- DestinationPidBank default is 2
- TuningDuration is 60 seconds
- SmoothQuickSource default is 25
- DisableSanityChecks disables certain checks that stop the PIDs from being written default is false
- Complete is set true after a successful AutoTune run.  It must be true for PIDs to be written to DestinationPidBank 

DataObjects.SystemIdentState
- Is logged
- Is not stored permanently
- Goes away when power is removed
- HoverThrottle is the average throttle used during tuning.  It is a good value to use in Settings.AltitudeHoldSettings.ThrustLimits.Neutral although it is usually a little smaller than it should be due to throttle bloom during shaking.
- The 3 values in Noise tell you how much vibration you have on the 3 axes.  Normal values range from about 100 to about 1000.  For high values, or jittery response to the PIDs created, you may want to increase Settings.StabilizationSettings.GyroTau (found in the GCS GUI at Configuration -> Stabilization -> Expert -> GyroNoiseFiltering) and retune.  Now you know how much vibration you actually have.
- Contains fields that may be useful if debugging problems with AutoTune
- Contains copies of some fields from System.SystemIdentSettings