I have a SEC box and I raised mine up. It is actually a little higher than the bed rails but that it the only way I mount it cause the bottom of the box hit the clearanceing for the gas filler in the bed.
To raise it up I put a piece of the angle with the holes in it across the bed to have the box rest on. I also put bolts through the back of the box into the bed. Then I put threaded rods through the bottom of the box down to the bed with some square stock around the rods for the box to rest on. I put nuts on the rods and tightened the box down onto the sqaure stock and it doesnt move.
You can see the square stock in this pic.