The proper way to clear the stored codes is to connect the test jumper, turn the ignition key to ON then pull the jumper while the CHECK ENGINE light starts flashing out the codes. This will prevent you from having to reset you climate control, clock and radio settings.
The procedure above is to clear the stored EEC codes. It will NOT extinguish the CHECK ENGINE light. As stated previously, the light is on because there is a condition preventing your engine control system from functioning properly; maximizing performance and minimizing emissions. Learn to read the codes and save yourself a bunch of grief. The CE light is your friend. Let it help you keep your engine running at its best.