> Do I use rtag again - only specifying "-r HEAD -b <branch>
> <explicit directories>" or something.
That'll work.
If your developers are using directories/sandboxes they shouldn't - then you need to control your process a bit more. And I'd personally make this the developers problem - they put the code in the wrong spot, get them to fix it.
If work has been committed regularly to the wrong spot (HEAD not BRANCH, or BRANCH not HEAD) for months, then your project manager is doing a poor job of watching the commits - make sure you are getting automatic checkin e-mails at least.
Finally - there is no such thing as a stupid or dumb question - but you can be better informed by spending a few dollars on one of the many many many good CVS books ('Essential CVS' is good, or 'All About CVS' which I had a hand in writing). Then you'll be able to answer questions as well as ask them.