On both of my trucks that I have used to tow the 5th wheel, I had running boards that allowed me to step up and reach into the tool boxes in each truck. The tool boxes are the type that sit inside the bed rails at the front of the pickup bed and are flush with the top of the rails. In my old truck the lid of the box was 2 inches above the bed rails. It never came in contact with the 5th wheel even in tight off camber turns.
This is the box I have in my current truck http://www.deezee.com/products/401/Truck_Tool_Boxes/Truck_Tool_Box_Chests/Red_Label_Utility_Chests.html