i had them go over the rails on the bed on mine... the first one i did stopped at the edge of the bed but then i found that i was still scratching the top of the bed. Now the protection goes all the way around the bed and slightly past the edge.
For instance it goes up the inside wall of the bed to the top of the bed, then covers that entire surface going outward, and about 1/2 down the outside on the body of the bed. I hope that makes some sense... it's worth it to get them to do it over the top. I also had them do my nerf bars because the gravel picked up by the tires had chipped the paint and it was starting to rust... i highly recommend this too, it adds traction, looks good, and protects incredibly.
Line-X is a must have for any truck in my opinion.