I have the 60 gallon RDS that I am pretty sure would fit under your bed cover.
When you say be able to fill without removing the bed cover, I assume you are ok with rolling the cover back, right?
If not, you should consider one of the replacement tanks (Titan is the one I hear the most about). I like the idea of saving bed space, but couldn't get on board with the cost for just a small increase in capacity.
For the record, my aux fuel tank is one of the best mods I have ever done to any truck. Sure is nice to stop for fuel when you want to, and not have to search out a station that can accommodate truck/trailer/boat when I am traveling.