I did that exact thing on an aluminum flatbed made by TG Mountaineer. I had boxes under the bed in front and behind the rear wheels. I had longer boxes on top of the flatbed between the camper tie down points. I had flip-up rings in the flatbed deck at each corner that I attached the happi jack turnbuckles too.
My truck was a dually so the bed was 8' wide which did require dually swing-out brackets on the front jacks. This still only left me with about 3/4" of clearance between the jacks. My fresh water supply hose connection was on the underside of the camper wing facing down. The toolbox blocked it. I made up a 90 degree fitting with some parts from the plumbing department of Lowes.
My flatbed was semi custom built. I really wasn't happy with the overall quality of the bed but they were one of very few vendors willing to customize it for me. I think the bed and boxes cost me about $6,000 in 2011.