I would recommend some form of bedliner, spray on or the bedmat suggested for the dust factor in the back, I do a lot of driving down gravel roads and I use a lot of weather sealing where ever I can around the tailgate especially to keep the fine swirling dust out from the start. It can be a real mess if you don't have anything for this.
Ford makes a tonneau cover that folds in 3 sections across the back that came on my 2015 F150, with lower profile dog boxes with covers on I can lock down the tonneau cover to the back and push the dog boxes underneath, it is very tight squeeze but they do not move around. I then have steps on each side of the bed behind the rear door that move in and out that I can step up on and reach over the side to let dogs in and out. I seems to work even though I am vertically challenged.
My pickup came with a rubber floor board across the entire floor if anyone has a chance to get that it is the best thing ever, no extra cost. I also invested in the marathon seat covers so I can pretty much open the doors and spray the seats and floor down with a water hose if I needed to. Not sure if the marathon seat covers are worth it yet, they are real heavy duty and stuff wipes right off. My kids have tested them out on several levels as the seat covers where more for them than anything.
Last I think this newer style of F150pickup and the factory tires are not made with much clearance underneath compared to previous models. So if you can put better tires on and lift it up you will be ahead of the game. I don't know if the clearance thing is to help them get better gas mileage, but I spent a few times last year stuck in the snow and ice where I know my 2010 F150 would have gone through. Just my $.02 hope this helps, it is a really nice pickup.