Spray in bed liner will be your best bet, if youre willing to do that as a permanent solution, since you have to destroy paint/finish underneath. Drop ins can get water and debris underneath and advance the rust. Some like bed mats or carpet, or a combination of a liner and mat, etc. I would shop around, obviously Line X is the best but I had my dealer do it for me when I purchased the truck, so the brand I got was whatever they use. The finish isnt too rough or things move so that I need a mat, but maybe in the future. And if you know what youre doing or have had experience you can do it yourself. I myself wouldnt but hey who knows.
I just picked up a cheap BAKFlip Fibermax Tonneau and it works great. I couldnt see myself paying the $900 price tag for it but for what I paid I love it. There are plenty of Tonneaus to choose from for tri fold, it really just depends if you want soft/hard, and how much you want to spend. Good luck!