I like to lay the top of the box along side the bottom. Then, anytime I am rummaging through the box to find parts, whatever I remove from the bottom goes into the top - not on the workbench, or a chair, or anywhere else. This way I always know that the part I am looking for is in one box or the other.

I also like to open all plastic bags and transfer the parts to ziploc bags, so I can re-seal them after removing a part.

For small screws etc, I have a magnetic dish to keep them in.