I have an RDS combo 40 gallon tank/toolbox in the bed of my F350 dually LB. It sits about an inch lower then the bed rails. I also pull a fiver.
Here's the way I looked at the situation and what I found:
Many hard cover tops seem to have framework that extended low enough below the bed rails that it would contact the tank, so I crossed those off the list. I think I also had the same problem with the hard top retractables. There always seemed to be components that would extend too far below the bed rails.
So next I looked at the foldable, stackable hard tops. Some of these might work, but then the rear window would be blocked during hitching and unhitching and I'd be running down the road with a rear view window that was completely blocked. Not something I wanted to do.
So I finally looked at soft top roll ups and that's what I went with. I'm very satisfied and a little surprised. For $300 installed, it fits tight and cannot be opened without opening the tail gate. Yes, a knife will do it too but I'm trying to stop the guy walking by and looking in every truck bed to see what he can grab. I have a Truxedo Truxport. Made in USA.
One thing you might investigate is maybe call RDS and ask if they will build a custom tank for you (I've heard they will). Then you could have one made up that is much lower then the rails. Also check out the RDS website - they have a zillion tanks.
* Remember that when towing, the cover will be rolled up, so access to the toolbox is not impeded.
