The pipes are easy. Just take down the existing exhaust. Bolt on the new head pipes. Then place the muffler ( with the hangers on) on the pipe. Drill new holes on the under side of you car using the hangers as guides. Make sure the mufflers are level and an even gap all the way back. The pipes should be hung before the rails and shields.
As for the covers, if you have rails that are already drilled, hold them to the car just under the door. Drill holes into the car using the holes in the rail as a pattern. Then slide the shield on the rail and screw it on the car.