Yes, the Power Commander is a "set it and forget it" type of device. It alters only the fuel injection, and on some Power Commander models can also alter the ignition timing. You alter a "map" that makes these changes. An optional feature available to ADD onto some Power Commanders is a self-tuning module that can recommend changes to enhance the air fuel ratio at different rpm and loading automatically, and the recommended changes can then be made permanent via altering the map to reflect them.
The Power Commander has NO effect on the Kawasaki dashboard settings. You can still select full or reduced power, and can still select the traction control setting.
You should make an effort to find out WHICH specififc model of Power Commander you have, and WHICH specific map was loaded into your Power Commander by the previous owner, as that can let you know what has been done and what has not been done to alter the fuel injection and ignition mapping.
It is important to not make either Power Commander map changes or physical changes (e.g. exhaust, intake)without "matching" them, as you cna do serious engine damage with improper changes.
Jim G