I have two approaches for my dogs. First, for occasional use or regular short-term use, I have this:
It fits a Superduty very nicely, fastens to the headrests on the front and rear seats of a 2012 crewcab Lariat, and keeps the dogs in the back seat plus keeps the hair and any accidents in their place. All you get is dog slobber on the rear windows and rear armrests and a little dog hair to vacuum on the sills. It's been used extensively and has held up well. Installs in about 2 minutes once you adjust it. And it's big enough to cover the full width of a Superduty, which most of the covers don't.
The other approach is to get a folding load floor for the back. It's not available on 2012's on, but you can find them on classifieds or just posting on these forums. Ford has them new, but they're $1000+; you should pay about $100-150 plus about $50-75 shipping for ones in pristine condition. Once you have one, get a Superduty-specific memoryfoam dog bed from this source:
Dog Beds - Dog Furniture - Orthopedic Dog Beds - Memory Foam Dog Beds from BigDogBeds
This guy has done a custom design for the Superduty with the load floor (I heard about this bed from a guy on another forum who had it made). It isn't cheap but it gives you a huge space for your dogs, contains the mess, is completely cleanable, and looks really nice. It has a custom durable dog print in a specialty seating fabric, memory foam interior, and everything is notched and cut to fit that back seat over the load floor just perfectly. The load floor makes it better for the dogs in all instances, regardless of what seat cover or custom bed you use. Even with a couple bath towels it's great, and it folds up right under your rear seat.