That resort fee also includes free internet access in your room, health club privildges and a newspaper at your door Monday-Friday. Thats a lot for $12 but not free!
You can leave your car in the hotel parking lot of the Disneyland Hotels on your final day, not sure about the offsite ones. Bell services will store your bags for you too. So when you are ready to go, get your car from Self Park and drive up to the front and have Bell Services load your bags in the car for you. Have a great trip!