There is actually no need to split up the geometries and textures (there are even advantages to have them all in one huge flat directory, avoids duplicates and indicates potential conflicts).
The way I have set it up is one geometry and one texture directory (in the P5 runtime).
Everything else is split over 9 runtimes at the moment (including one used as a temporary staging one). Things are moved around as required. For me CRPro is the best tool ever as it allows me to move things around and have all references fixed automatically.