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Not sure I qualify, but I have a Bakflip MX4 and a Bakbox and it's a fantastic combo. I keep tools and gear in the Bakbox. It's a little smaller than a traditional bed box but it's locked under the cover, and you can even collapse and stow it away if needed.
I have the revolver X2 and bak box. So far it does the job but I may mod the mount with some sliding drawer fittings so I can slide it closer to the cab when I need to use the box link mounts. There's a thread about it but the OP doesn't seem to be active anymore.
I can't remember the name of it, but when looking for a tonneau I came across a make that was specific for toolbox. It basically started behind the toolbox.
other options would be a bak and bak box combo or get 1 or 2 undercover swing boxes? Depending on what you need to do with it
UPDATE: http://www.accesscover.com/toolbox/ this is similar to what I saw. Tonneau starts after the box.