I just installed a local mfg tank (12wx18hx60l 55gallons). I pull my fuel off the bottom drain at the botom bottom bottom drivers side corner. I had them put the drain there so water would not accumulate under the drain port in the tank. I also have a RACOR 690T fuel filter / water seperator as the first thing out of the OEM tank going into the fuel system. With the extra aux tank I would definitely would want some way to filter water and particulates really well before it gets into the fuel system, yet not have to pump (electrical connections, switches etc)it through from the aux.
Then I went through the bottom of the bed because it is gravity feed. Don't forget to allow for a shutoff valve. I clamped the hose to the top of the bed bottom using those metal stainless steel rubber insert clip type clamps that you can put a 1/4" bolt in the mounting hole (the kind of ones you use to secure cable to a wall, just the metal ones not the nylon ones). You can use an extra clamp on each end of the shutoff valve to physically strap it to the bed so the valve stays put.
Make the hole big enough to pass the line AND fittings you are using. I also allowed room for a grommet to keep the hose from having mechanical interfearence with the sides of the bed hole. Remember you are opening up the bed protective paint cover to rust, so use some kind of a sealer to keep the hole edges from rusting before you put the gromet in. The hole becomes no small hole after it is big enough for the hose, fittings, gromet, so have a place that the hole can be big enough. I used a "step drill" and went to the about 1 1/4" step.
One thing to check FIRST is underneath the bed cross bed support structures and measure where they are. You do not want to start drilling holes in the bed to only find you are trying to mount your stuff right over a bed support member and have to work around that thing.
Knowing it is going to rain sometime in your truck's lifetime with this tank in the bed, make sure the water that goes down through the place the fuel line goes through the bed is not going to pour water on anything else (especially electrical) you may have mounted under there.
I have been having a problem on my 02 with the Vp44 0602 code if the OEM tank does not have any dead air space (ie the OEM tank is slam full). I only get the code if the aux tank has totally filled the OEM and the VP44 return line I have in the tank vent line is under the surface of the fuel. Once the aux is shutoff and the OEM starts to drain down and the VP44 return line in my tank vent line become uncovered (exposed to air) the code stops being set. It is repeatable, VP44 return line can not vent, sets 0602, Vp44 return line can vent, no code. I am going to go with the Northern Equipment check valve that mounts in the large fuel filler hose that will keep the OEM tank from filling slam full (ie only to the point of the check valve (which I will mount as close to the tank moulding as is physically possible)). That should take care of the 0602 problem as well as allow for same thermal expansion.
I think what is happening is I have some air comming through a fuel fitting somewhere, the VP44 is trying to expel that air but is working against the liquid fuel level and is not able to expel the air as easily as it should. When the VP44 return line can "see" air the code does not set. The code only happens at idle (800 rpm, ie the intermediary internal pressure of the VP44 is not really dumping fuel out the VP44 byass valve at a high rate) and not at any throttle advance at all. It also has a characteristic of running rough like an injector not opening / closing correctly. Vp44 return sees air, problem (0602 code) immediate stops happening. What I suggest is let the aux drain, but have a way it does not slam full fill the OEM, hence the Northern Tool check valve in the main fill line is how I am going to approach that.
Oh, also I think the shutoff valve needs to be designed for fuel (ie not the regular standard water ball valve from a plumbing supply because the fuel could deteriorate the nylon seal or o-rings). Auto parts stores have fuel shutoff ball valves designed for fuel.
I have run about 200 gallons through my aux and love it. I love shopping around for fuel and able to pickup 30 - 40 gallons when it is a little cheaper.
Just some thoughts,
Bob Weis