Normally when you install UT200 it is installed to your /home/username/ut2004
Not sure why you have it installed to /usr/local/games/ut2004 ?
If it works for you .... then okay.
To update the game from a patch you need to copy the patch files over the existing install.
The easiest way, if you are getting a "permission denied" error is to log in as root and copy the files that way.
Just make sure you do a chmod 777 on the patch file first