I have the Fold-a-cover with their toolbox. It works great, and I have had no issues with it at all. To be fair it is the first tonneau cover I have owned.
As usual I did a TON of research before buying it. I too came up with the fact I was going to get a folding type fairly soon on.
I like the fact that the forward panel flips to the rear, so I can access the toolbox easily. I store all my tools and repair stuff in their, plus a bunch of other small items. The only drawback of this is, is when I am towing and have the rear panels folded up on top of it, as it is then inaccessible. This has never really been a big deal, just the one wee negative to this setup I have found.
The toolbox hangs in place, with the bottom about 6" off the bed of the box, which allows longer items to be placed in the box.
I have had it installed for 8 months now, and have not had a single leak that I know of, everything including the stuff in the toolbox has stayed completely dry.
I had to take a leap of faith, as I had not seen one in persons, but it met every expectation I had for it. I had looked at the Bakflip which is available locally, and though it is a great product, especially given it is cheaper, but the Fold-a-cover in my opinion is a better product, and the toolbox was the clincher.
With the Fold-a-cover you can open the tailgate separate from the cover, something which is nice if it is raining. Though when towing my fifth wheel, I don't put anything in the box (with the exception of the toolbox which is always covered) that I don't want to get wet.
I would bet it took me just over an hour to install the cover, and another 30 minutes to install the toolbox. Next time it would be faster.