How to host a dedicated server
See the following forum posts. It explains how to set up a dedicated server for Linux and also Windows based systems to be controlled through automated scripts and where to change settings.
The post also explains the manual way of handling a server directly using the console without scripts in the spoiler section at the end of the post.
http://games4linux.de/howto-running-with-rifles-dedicated-linux-server-erstellen/ (in german/auf deutsch)