I think the key to organizing is to limit what you carry. I love to have tons of everything but over the last few months I have been using it all up and just getting better with getting stock for the jobs I am doing and returning whats not used. I have tons of stuff in my garage that just equals wasted money. I am not near my garage when I need it so I end up buying it again.
Inside the van I have a shelf on each side in the rear and behind the drivers seat is open. On the floor are 1 case of 4sq deeps, 1 case of old works, and the power tools.
It is nice having the van open to load stock in for a job. I keep 2 4' ladders inside all the time and limit carring the extension ladders to when I need them. Saves on fuel and so will a lighter van.