Its tough, trust me.
Top deep drawer for sockets, ratchets, extensions, and all the other good related stuff.
First skinny drawer for wrenches. The one under that for pliers and/or screwdrivers.
Bottom big drawer is where you keep things like a come-a-long if you have one, a sledgehammer, maybe knee pads or a kneeling pad, gloves, etc. Its more of a storage drawer.
Bottom left big drawer is good for chemicals and cans since they can stand upright.
After that, youre pretty open to how things feel for you. I just set most of my boxes up the way I described. Its more natural feeling.