The further a shadow goes into space the lighter it becomes. Google, aerial perspective and read about it. Also, if you do this traditionally you will get a better understanding. Analysis done with traditional mediums will give you more knowledge. Digital painting/drawing is an "imitation" of traditional mediums. You're doing fine starting with basic geometric shapes. Do the same with the mediums - start with the most basic ones.
HideraHiberna, one problem is that your original boxes aren't correct, at least as far as I can tell. The rightmost box is fine, but the leftmost box has vanishing points that are really close together, making it seem like its top is not rectangular, but more diamond shaped.
The issue of where to place vanishing points is one I've been investigating recently. It turns out that for classical perspective, they're not evenly spaced! See this brush for details.