Safety first. If you bump into something there's a pile of stuff just itching to clobber you in the back of your head (unless you have a bulkhead or net).
It's up to you really, but I feel it sensible to keep things I use frequently near the door(s). You'll find it's more important to organise your toolboxes properly which will save popping out to the van just to get another tool. While with many jobs it's impossible to take everything in/out in one trip it's less professional to keep running out just to get one item. Also, it's important to keep things neat and tidy with everything having a home so you spend less time looking for something.
I have a general toolbox for wrenches, screwdrivers, stanley knife, pencils, pipe slices, etc, another for soldering, another for demolishing/making holes/carpentry, etc. I have toolbox organisers to keep my fittings (15mm in one box, 22mm in another, HEP2O in another, etc., large plastic containers full of traps, washers, solvents, etc.
There's a fair amount of space in the front to use too. On the front seat, paperwork including brochures, the last three weeks of newspapers, empty sandwich cartons and sweet wrappings, coffee soaked banana skins and the windscreen holds an impressive display of around 300 post it notes ...