I use an app called Folder Organizer to create my folders. It allows you to use custom icons for the folders etc. it has a back up feature but it will only back up the folders created by the App. On my Eris and Dinc the back up was stored on the External SD card so switch ROMs had no affect. not sure if this will work with the Gnex since there is no External SD card. I am not rooted so I cant test it for you.
Not sure if this helps your or not, but thought i would share. Good luck.