The one thing I've found lacking about the CVS documentation, is that it is not so simple to understand that you really can't take an existing moodle install and turn it in to a CVS install that you can update using cvs update -dP. You HAVE to start with a "clean" CVS install, then update it with cvs from there.
If you want to change your existing moodle and make it manageable by cvs, you need to follow these steps:
Step 1: Backup your database
This step is NOT optional as I've found on several occasions. Upgrades usually go smoothly but when they go wrong - it's a real roller coaster ride.
Step 2: Backup your existing /moodle/ folder
Again, just in case. You'll appreciate this is something goes wrong. In Ubuntu (or any *nix), it's a matter of mv moodle moodleold
Step 3: Follow the instructions on "Installing and Managing Moodle via CVS"
I can see you've read the instructions, but, the commands go like this:
cvs -d:pserver:anonymous@uk.cvs.moodle.org:/cvsroot/moodle login
cvs -z3 -d:pserver:anonymous@uk.cvs.moodle.org:/cvsroot/moodle co -P -r MOODLE_19_WEEKLY moodle
I've chosen the uk server since it looks like it would be most appropriate according to your profile. This step takes a while...Step 4: Make the new moodle install your own
Copy over your config.php file, non-standard themes, blocks, and modules into their respective places.
This step can be particularly troublesome. If you discover that you end up with a "white screen" after the move, then delete your non-standard themes, blocks, and modules. Check your site again (should be the standard theme and you're probably missing your non-standard blocks and modules, but, it should be working), then carefully add individual non-standard elements until you figure out which particular element (theme, block, or module) is giving you trouble.
Using http://yourmoodle.edu/moodle/admin/blocks.php and http://yourmoodle.edu/moodle/admin/modules.php will help to make sure that you haven't forgotten anything.
Step 5: Done
These four steps should leave you with a "new" moodle install that you can manage with cvs.
Happy Moodlin!
-Geof