It's probably not necessary to quote my entire post.

First of all, hopefully you're the owner of your computer. If you're not, you shouldn't try to mess around with the inner workings.
If you ARE the owner, then here's what you need to know: Linux, by default, protects operating system files so that they can't be messed up. Anything you can't change easily is something that you shouldn't change without knowing exactly what you're doing. Before you make any changes, be sure you've done your research, made backups, etc.
Now, having said that, if you only change stuff in /usr/local/games/tremulous, you're unlikely to mess up your computer in any serious way.
To change protected parts of the file system, you need to use the
sudo command. This is used on the command line as a prefix to a normal command. If you use sudo, the computer will prompt you for your password. Entering your password will cause the command to be run with root privileges.
For example, say I have my new server.cfg on the desktop and I want to copy it to /usr/local/games/tremulous/base. It might go something like this.:
~$ cd /usr/local/games/tremulous/base
/usr/local/games/tremulous/base$ cp ~/Desktop/server.cfg .
cp: cannot create regular file `./server.cfg': Permission denied
/usr/local/games/tremulous/base$ sudo cp ~/Desktop/server.cfg .
Password:
/usr/local/games/tremulous/base$ ls -l server.cfg
-rw-r--r-- 1 root root 5292 2007-10-15 14:25 server.cfg
/usr/local/games/tremulous/base$
Sudo is VERY POWERFUL and DANGEROUS. The general rule of thumb is, only use sudo when you absolutely need to. That way, it's harder to accidentally mess something up.