All my boxes are arranged the same. If it is a top box, the top is sockets, extensions and if possible ratchet handles.
If it is a bottom box (with a work top) these usually have a 4" deep drawer on top for sockets. If not, you can often rearrange the drawers to suit.
2nd drawer down is always screwdrivers for me, then pliers, then wrenches. Typically the drawers get deeper as they go down. That's where I keep my bulkier items.
You can make your own foam cutouts pretty inexpensively. Here's what i do:
I buy 1/2" thick camping mats for under sleeping bags. They are 2' wide and 6' long for sometimes less than $10.
Cut to fit drawers- Then I cover them with blue painters tape (or at least where I want the tools to be). Then I trace around each tool with a sharpie. Cut to the line with a straightedge and a VERY sharp pointy x-acto knife. I actually sharpen the blades from new. Mine are like scalpels. Not hard to do and it really helps you turn corners.
The foam mat can be glued together with Super77 or any headliner adhesive. I buy this colored foam at the craft store and glue that up from underneath to provide contrast.
A couple tips:
1) you can't put sockets too close together. But having a glued on bottom helps stabilize the thin sections of foam between tools.
2) I like the holes for sockets SLIGHTLY undersized.
3) No shapes need to be perfect. Imperfection in your cutting just makes the tool fit that much better
4) Don't forget holes for fingers to pick the tools out of the foam. I made beautiful cut-outs in 1/2" foam for 1/4" amd 3/8" extensions, then couldn't get them out.
5) in aviation boxes, wrenches are typically stored on edge, not flat.
6) I have found it best to try to cut out the entire shape of the tool. I leave it in place for when I spray on the glue to protect the inner surfaces of the cut outs. It also helps hold the shape of the foam while the glue dries. Just push the cut outs up slightly to avoid contact with the base material.
Just an idea: You don't have line the entire drawer with foam. If you could find a shallow cake pan, tupperware, or even a sheet of something rigid (plywood, hardboard, plastic, aluminum?) you could glue your foam to that. Rivet on some thick magnetic strips and you have your own version of mechanics times savers that can be removed from the box. You could do whole sets- 1/4" drive with ratchets, sockets and extensions for example.
The foam cut-outs are time consuming to make, but look and work great when they are done. Moreover, they force you to seriously consider what tools need to be in your box and what tools belong elsewhere. In aviation, every single tool has a home and the homes are serialized for that tool. We don't really need that for automotive. But it would be nice to have the drawers I mentioned done. I have found mechanics' screwdrivers in my car interiors. Wonder how long they looked for them. This happened to me a couple times and both times, I called the shop and returned the tools (naturally). In aviation, we put away our tools each day and account for every tool. Auto mechanics could do he same.