There are a couple of companies that make covers specifically for trucks with tool boxes, like the one shown above. Problem is, then you gotta buy a cover all over again.

Get a regular toolbox and modify your cover to work. Get creative, that's half the fun of moddin'...

 

I just got rid of a craftsman crossover box because i wanted to go with a tonneau cover. I got the extang trifecta so it folds up 1/3 of the bed in about 20 seconds. I went to tractor suppy and got a 100 dollar locking plastic box that sits down in the bed. Went out and bought these corners that have tabs on the bottom that fit down in the bed liner and hold it in the middle of the bed. I had the box ratchet stapped in the front of the bed but to access it I would have to unstrap it every time in need into it. The blocks that hold it in place cost like 10 bucks at sears and keep in right in place w/o having to remover the cover. I'll take a picture when its not snowing and 5 below outside.