Your Knock levels will go down after a tune. If your car is knocking under load it could be leaning of a little. Your tuner will add some fuel at that point in the map, you can use the map tracer function your self to find exactly where in the map your car is knocking. The tuner could also retard the timing a little to reduce the knock.
Like TonyGTST said: Your knock sensor on the pfc is only really usfull when the car is idling, its main function is only to tell you if something is really wrong when first installing the pfc.
ps, when driving if you see the engine warning light come on back off staight away or you risk a blow out....
hope that helps.