Yes, the rear fender resessed area should be covered with the running board. I would put the front fenders on and then put on the running boards. Then just put the rear fenders on to fit up with the running boards. The rear hieght of the fender is up to you, I put them so that I have a couple inches of clearance on the top of my tire. The bottom rear of the fender is almost even with the top of the rear frame rail on my car.