I manage a very large used car dealership and get a demo vehicle to drive as my daily. Obviously, as a truck guy I usually take out different trucks. I've probably had hands on time with every tonneau cover known to man. When it came time to buy one for my own truck it didn't take a second to decide to go with the Truxedo TruXport tonneau cover. It is an incredible buy for the money. I got it on Amazon for $266 and free shipping. Pretty much waterproof, very low profile, rolls up and out of the way very easily for hauling tall loads, and looks great.
My Raptor already had a DIY roll on bed liner. The coverage is inconsistent, so I'd recommend you have it done professionally. Not to say it can't be done right at home, but there is usually a noticeable difference between home jobs and professional ones, IMO.