Setting up the project structure

If you are going to symlink your files in the project directory, create it in /
(eg: /cvs or /configs).

If managing configs for multiple machines, you could set up:
config
server1
etc
server2
etc
server3
etc
...

Copy the files from their "real" locations to your cvs project.
Import them into your CVS repository (/home/cvs).
Then, check them out into your project directory (/cvs).