Looking back over my reply I'm probably telling you more than you want to know.  I've had service beds on everything from a Ford Ranger to a Chevy C-60 and used them in the propane business and farming.  Over the last 30+ years I've set up (as in start with a bare service bed and organize and fill it) 8 or 9 trucks.  There's two main factors: 1) how it will be used and 2) the personality and habits of the user.

I'm going to make an assumption here:  You will be using the truck fairly close to what you are working on.  In a lot of my work in the propane business that wasn't the situation.  And it has affected how I organize trucks. I tend to make go kits for power tools or activities.
Milwaukee Packoutor Dewault Stackable  are my favorites. 
The tool and accessories are in a box you can grab and go with.  Your drill has all the bits and a spare battery (always carry a spare battery).  The half inch impact has the impact sockets you normally use.  The Hackzall has blades.   It works great BUT it takes more space.  I could not do that in the Ranger with a 6 foot bed.  My C-60 with a 12 foot bed allows it a bit more.

In the propane business there were recurring jobs.    I knew for this job I needed those tools.  So I had little kits I could grab.  Testing pressure at an appliance I usually needed a 1/4" hex, 3/8 or 7/16 wrench, adapters and a gauge. So those were in a small box or pouch.

Part of the decision is what your bed is like.  I had a 10 foot crane bed with a flip up top on the left side.  It was great!  Downside was you couldn't mount anything on top of the side, but it was where I carried bigger wrenches (I carried a 36", sometimes a 48" & 60" pipe wrench on that job) and supplies.  OK back to how to set it up.
  
Start on the driver's side.  The first compartment is tools you use most, probably most of your tools.  Most dealer service guys have their big tool chest in the back of the bed.  But the truck is the company's and the chest and tools are theirs.  Downside is it ties up the bed.  It may be that is how you want it.  I want the bed open for wheels and tires, blocks, big things or things I don't always carry.  The Montezuma type toolbox is good.  I have the John Deere version chained in the bed of my pickup (make theft as difficult as possible).  Never tried one inside a service box.

The first compartment is tools you use all the time.   Something I saw I've not duplicated yet was a wrench rack on the door.  They welded rods on a steel strap like a Montezuma box and mounted it in the compartment door.  All the combination / box end wrenches  were organized hanging there. Open the door, there were the wrenches.  BUT they put a piece of angle iron on a hinge over them as a retainer.  So when you finished you dropped the the retainer and the wrenches didn't bounce out going down the road.  I LOVE the idea.

On my C-60 the first compartment is a chest with tools (wrenches, sockets, scewdrivers hammers, etc).  Hanging on each side are bigger wrenches, pipe wrenches, etc. The bottom shelf are my power tool kits

Next compartment is (unless you have a longer bed) the one over the wheel. On my trucks this has always been supplies.  For the farm mostly bolts. Get a set of drawers for bolts. I like these myself. You can get them in various sizes.
 (Be sure to measure your box depth.  They are not all the same.  And box design may limit how you use them.  We screwed them on two 2x4s to raise the bottom row to clear the edge of the door.  If the compartment is big enough this is a good place for other supplies.  Penetrating oil, wire connectors, duct tape, etc.

On mine there is a crane on top of the left side.  My preference is it be on the right but this is how it came.  The back compartment is where crane stuff is stored.  Control cable, chains, hitch inserts (truck has a 2" receiver. Removing the insert prevents banged shin bones), hitch pins, etc.  It's also where the long pry bar and big sledge hammer go.  I prefer it on the right side for a couple reasons.  One is it ties up the box under it (depending on the crane design, the old green truck had a post through the box)

The right rear is a et of drawers mounted in the top half of the compartment. It carries less commonly used supplies.  I'd prefer this be on the left rear but there's a crane there.  It holds various stock hoses and such.  The bottom is where I carry gallon jugs of engine and hydraulic oil, etc.

My middle right is grease gun, air fittings, etc.  There are hose reels mounted on top of the box plumbed into the air compressor and oil tanks.  It came set up that way but for our use we don't need to bulk oil.  I'm considering removing the oil tanks and reels to gain space.

You may want to to configure things to match what your doing. I try to check irrigator towers twice a year.  Check tire pressure, drain water off gearboxes and fill.  I throw in a couple wrenches and a box of towels and everything for that work is right there.

The front compartment is welding supplies and equipment. Oh, the welder and air compressor are mounted between the bed and the cab.  They guys who built it did a very nice job.

Be sure and mount lights inside and outside the box.  Inevitably you will be doing service work in the dark.  Put master switches in the cab.

One other thing.  Try to have all cordless tools use the same battery.    It makes life a lot easier.