Diagram from Wikipedia entry: PID Controller
To use the Autotune function, first let the cooker pre-heat and reach setpoint temperature. Auto-tuning works best if the system is already at a steady-state. The "Run" state will not allow you to invoke the auto-tuner, unless you are already within 0.5 degrees of the setpoint temperature.
Once the cooker has stabilized at or near the setpoint, press the RIGHT and SELECT buttons simultaneously. The backlight will turn violet to indicate that you are in autotune mode.
As mentioned before, auto-tuning is not perfect. With some practice you can probably get closer to the ideal tuning for your cooker. There are many good resources on the web that explain PID tuning.
To tune the Kp, Ki and Kd parameters, use the RIGHT button to navigate between the tuning screens. The UP and DOWN buttons will change the value. Pressing SELECT while also pressing UP or DOWN will change the value 10x faster.
One thing to be aware of is that the temperature control on a rice cooker is non-linear and asymmetrical. You can apply heat, but there is no active cooling. As a result, most rice cookers take a long time to recover from a temperature overshoot. For this reason, it is usually better to aim for a slightly overdamped response to avoid overshoot.