I put an ARE tonneau on my 2002 Silverado a couple weeks after buying it. I also put a Bedrug in the bed and sold the bedliner that was in from the factory. It made the whole bed into a giant carpeted trunk. That's not for everyone, and it limits the use of the bed, but after having friends and family borrow my prior pick-ups, this eliminated that. My tonneau was color matched and the truck looked good, provided safe and secure storage for whatever I put in there, and even though the truck is rotting away, it's still doing that job today. Mine also locks the tailgate if I lock the tonneau, but that is of questionable security. My truck preceeded locking tailgates, so that was a nice feature when I'd load up the bed going to the range for the day. If I did this again, I'd look hard at the UnderCover tonneaus. They are sturdy and you can stand on them if you need to. Makes a nice mobile platform for some jobs. Neither of those will work with a traditional toolbox though, and you'd have to reorient your storage to something under the tonneau that you could access when it's open.
Another option is one of the roll up covers. they have powered ones, and rigid, sectional ones, and you can configure it around your toolbox. You know you aren't the only one to want this, so I'm sure options exist.
