Well, I hate per-project audio folders, I love managing my assets, and I use the CWAF tool.
I did a massive re-org where I opened ALL my files, used the "copy audio to folder" option and set a manual audio folder in a heirarchy that worked for me. After doing this for everything I nuked hte original repository and now I'm golden. I use CWAF once a month or so to clean up dead wood.
Backing up, I just copy all my project files and folders to an external drive. I do a softer backup more frequently of just the project files to a partition.