I got mine on top of the dodge under the rail bed liner.
The difference is I also have 5th wheel hitch rails bolted to the frame, then I had to build a system to support the slide in camper higher then the 5th wheel rails. when I built this I made it so there is a piece of wood on both sides of the 5th wheel hitch (both rails) to keep it from moving forward and back.
Now my 5th wheel rails are sopported by about 6 washers under each bolt, and mounted on top of the bed liner. I drilled 1" holes where each bolt passes thru the bed liner so I could get the washers in for spacers. the 5th wheel system has 4 years on it, tonight I pulled it off so I could remove the bed liner and look underneath it. Looks great, no scratches or rust!
The trick is when ever I drill a hole thru my truck, I seal it with Coraless (spelled wrong) from Eastwood. That stuff is the best for preventing rust.