Put a piece of plywood that spans across the rails and about 2' wide. Staple the rubber bathroom carpet on it or screw in rubber bed liner material so the dog does not slip around and has a bit of cushion under him too. He gets to see out of the topper windows when he is lying down too. I store my emergency stuff under the rack. I use 5 gal plastic pails and put chains, etc.. in them. Spare trailer tire, lug wrnenches, etc.. extra clothing in a bucket too - it all goes under the rack.
BTW if you have a bigger dog or 2 medium dogs--you'll need to double up the 1/2" plywood because of the weight, so screw it together with 1" galv screws. Cut the second piece of plywood about 6" shorter and it goes under the longer piece. Make sure you use enough screws, and do it BEFORE you put the carpet on, eh.
Getting the rack in can be a hassle, but worth it IMHO. If you have side opening topper doors--it is real easy to do. If not I removed the window screen and slipped in the rack and reinstalled the 1/8" rubber rope that holds the screen in place. Place a topper hold down on the back side of the rack so when you accelerate the rack does not slide backwards. Actually I welded a "tab" of 3/8" x 3/4" to the metal hold downs to it so the rack would not jump it and slide backwards.
Bottom line is the dog is more comfortable and happier, and I can store more stuff in the truck. I've done this for the last 4 trucks I have owned. Works slick IMHO.