I organize my files a bit differently. This is because I use Vue on both a laptop and desktop computer and I want all my files available to me on both devices. So I set up a folder "C:Vue" which contains a bunch of 'my' folders and looks like this:

C:Vue
--- MyAtmospheres
--- MyBitmaps
--- MyDocs
--- MyFilters
--- MyFunctions
--- MyMaterials
--- MyObjects
--- MyPlants
--- MyScenes

Anything which does not come preinstalled with Vue, goes into a folder in these folders. I typically have folders within folders as well. For instance in my 'MyAtmospheres' folder I have the following folders each with different atmosphere presets:

C:VueMyAtmospheres
--- Bad Weather
--- Chipp
--- Cornucopia
--- Lush Atmospheres
--- Monsoon Atmospheres
--- Overcast sampler
--- SkinVue2
--- TerraAtmospheres
--- thomasKrahn

This way, I only need to synchronize one folder between the two computers: C:Vue

FWIW, I use Allway Sync on Win XP to manage the synchronization. I also use Allway Sync to backup my C:Vue folder to an external hard disk-- and I explicitly set it to NOT PROPOGATE DELETED FILES. This way, just in case for some unexpected reason my sync gets out of control and deletes some/all files between the 2 computers-- I still have a backup.

That said, I've never had a problem with Allway Sync deleting files.

HTH,
Chipp