I purchased a Rollbak canister style cover. I like it. It fits flush with the top of the bed. I was able to keep the wing by using spacers and lifting it up at all four secure points. I used nylon oil pan plug washers to raise it approximately 3/16". It is seemless and you cannot tell that the spacers are there.
The canister is located behind the cab and allows the aluminum slats to roll up with one-foot incremental stops. When open, you have almost the whole bed to carry something. The cannister is only about 10" deep, so there is room underneath it in case you are hauling drywall, paneling, etc.
I carry my dog in the back of the truck regularly, and it is a snap to open it, slide it back, it has a spring rollup device like a blind, and put her in the back. The release handle requires the tailgate to be dropped, so with a tailgate lock, it provides secure storage.
It is not, I repeat not, totally waterproof, but sufficient for most purposes. I like the capability it gives me more than ensuring a watertight bed. The cannister has built in drain hoses that drop out the bottom of the bed.
I found it on the internet at an aftermarket truck accessories site for $850 plus shipping. I then went to the vendor that did the Rhino Lining on the bed, and got him to sell it to me for $900 installed.
If you go to the Rollbak website you can review it. Installation is really very easy on any pickup but a Dodge Ram. Oh yeah, that's what we have! I wasn't aware of how bowed both the bed head panel and the side rails are, but they are not perfectly straight. This just calls for the judicious use of shims, and takes some back and forth adjustment to get both sides right so that it slides back and forth without popping out of the track.
The cover is flat black and looks great on my Flame Red truck!
Good Luck! You have many choices out there.
Jim