That's kind of what I do, but not "layered runtimes." I have a runtime called Animals. In the character folder I have fish, dogs, cats, horses, bugs,  fantasy (dragons and such), etc. Then under dogs I have separate folders for mill dog and the old Poser dog. Characters based on either go in the matching folder. Then the props folder is a similar set up.

Thanks to Daio, my most extended directory is under horse. :-)

Hope that helps!