There is a standard Drupal (and maybe everywhere) methodology for managing a project in CVS, but not all of us know about it.
- Always do new development on HEAD.
- When the time comes to leave a branch behind (as when beginning Drupal 7 development) branch off the old (like D6) stuff. Continue working on HEAD.
- You can apply patches from HEAD onto other branches, if you have other branches going.
This is the approach described in the fine Pro Drupal Development.
Please add to this.