I would say I have had a variety of combinations over the years and I like the soft covers. My current truck has a spray in liner ( previous owner) which is nice, and I bought my new cover for $230. I see the market is flooded with different variations of frames, but bottom line is they all work fine. I have an X-Tang currently on this truck and like it well. If you want a front tool box they make short covers to work with them.

Been using tonneau covers on my trucks since 1989 :-X22

Try Torza cover
 

I bought my Torza Tonneau cover and its great.....it has four latches that hook under the bed rail....I can fold it back one section when pulling fifth wheel and still keep items cover under bed....Bought on ebay 350. Its a nice look on the dually

Take a look in my gallery I have some photos of my tonneau cover. Its a regular pace edwards roll top cover.

also note, when installing the cover I had to cut come portions out of the bed liner to make it fit.