We do something similar, but the directories are on the server, and not on the local user's machine. So if I change anything, the new stuff is automatically available to all users, and I don't have to do anything else.
I have to admit, the places Autodesk sticks customization files drive me completely batty. I guess they were trying to be "XP Compliant", but it seems like a disaster to me. It's always difficult to remember if Autodesk puts a particular item in userhome/ApplicationData, or in userhome/Local Settings/Application Data, or in allusers/Application Data, or wherever... And now, with C3D, it's even worse, because now userhome/Application Data contains both an "AutoCAD Civil 3D 2008" directory and a "C3D 2008" directory. What a mess.
Things got SO much simpler when I moved all customizations to a single directory on the server.
This creates a little problem for laptops. A lot of the customizations are database files, and by default, it is impossible to use Windows Synchronization on these files. I think we found a way to enable Windows Synchronization for it, so all the files were copied to the laptop and available when the laptop was not on the network. But then our only laptop died, and we haven't gotten another, so I can't remember what all I did there.