If I may?  Leave the Geometries and texture folders be.  Most items in the libraries folders can be moved about BUT some of the newer e-frontier/Smith Micro content has the OBJECT file(s) located IN the library folders.  That is to say, the obj file may be in the same folder as the CR2 - actual character folder.  These items shouldn't be moved unless you want to edit the CR2 to point to the new destination folder.  I keep Poser 1-4 folders, Poser 5 folders, Poser 6 folders and DAZ folders with all of the various content in sub-folders below those folders.  The DAZ sub-folder is further  broken down into sub-folders containing clothes, etc for each of the figures.  Poser 6 also has Ben, James, etc. folders.

I keep a pretty structured Runtime and don't have ANY trouble finding anything.  Well, let's face it, we all have brain farts once in a while.  I do maintain a couple of runtimes containing stuff I don't normally use and even a couple of "project' Runtimes.  Whatever works for you.  It is handy to have everything you need and nothing else in certain runtimes.

Start looking into your cr2s and pp2s and you learn that not all providers are all that careful about path statements, especially freestuff providers (bless them all).  That DOES add to load times.  If path statements to textures are correct (or corrected) items will load faster from the Library palettte.

I think I could (and have) spent hours and days just organizing runtime content.  Maybe I'd spend LESS time just hunting and pecking for what I'm looking for.  Now where did I put that Row of 10 Books prop ...