Using CVS to track changes to system binaries isn't really practical. Although it will work, CVS doesn't handle changes to binaries in a way that lets you diff or merge, so it won't provide you with useful information. Unless they've changed the functionality and I just haven't kept up... If you want to track changes to the binaries you compile and deploy, you can keep the sources you compiled from and back them up somewhere else.
CVS does work well for text files so you could manage directories like /etc and /usr/local/etc.
Either way I don't recommend checking out to the root of your file-system. Check out to a working directory to work on managed files, then check them in again. When you want to deploy files, you can export them to a temporary location and move them from there. It sounds like extra work and I've probably made it sound that way because I'm against it