I'm familiar with the issue you are working on.
My new CM flatbed came with two knockout panels on the driver's side of the bed, one forward for a midships fuel tank and one at the rear for the rear tank. I decided not to use the knockout because the fuel filler neck would have to run 2' or more in a horizontal orientation. I thought this would be very inconvenient. It would cause slow filling, splash back running out, and would require holding the fuel fill nozzle for the complete tank fill. . . the fuel nozzle would fall out if left without human assistance.
I had the bed installer cut a perfect circle in the bed deck and run the fill neck verticle from the tank. It works great, fills easy, and I can insert the nozzle and walk away. Using the kit provided with the bed the fill neck is recessed below the surface of the bed deck leaving the bed without obstructions.
New CM beds come with a thin stamped steel "cup" that drops in the opening and, in turn, contains a smaller diameter opening in the bottom of the cup for the fill neck. The package also comes with a length of thin metal tubing, same diameter as the factory fill neck and maybe clamps as well. You might be able to buy the kit from a CM dealer. . . you can call the company and ask for a dealer near or nearest you. CM has a good website. Transfer Flow in Chico CA, a TDR advertiser, also sells the same kit to use as a pass through for owners with tank mounted beds under a camper shell. TF also has an excellent website.
I wouldn't run the fill neck horizontal out to the side of the truck.