Other than engines, I store the boxes under my layout. It is well organized from a structure perspective, but I have no idea what is where.
If I were to want to thin the herd, then I would likely grab boxes and see if I could find the car, and determine if I wanted to sell. Taking a car and then trying to find a box would be fruitless.
I keep my engine boxes upstairs in my attic. This makes it easier to find if I need to send an engine back to get serviced.
John