I agree that you want the most used tools in the top and then sort by size with heavy stuff in the bottom. However, tool box organization is a personal thing. You might want to organize your tools by purpose. All automotive tools in the top 4 drawers. Cutting tools in the next 2 drawers and plumbing in the next, etc.
Something else you may want to consider are some tool organizers so you can keep all of your sockets, open end wrenches or box wrenches organized by size in your tool box and then be able to grab the whole set when you need to use it somewhere. There are all kinds of organizers like this.
Once you are all done organizing your tools in the tool box you may want to label the drawers so it is easy to find everything at a glance.
You will love having a large tool box. I couldn't get along without mine anymore! I kept my old carry around box for those situations where You have do something away from home such as a friend needing some help at his house or someone in your family stranded on the road, etc.