Elite Force can be configured to quite some extend and in different fashions. As the game is derived from Quake 3 Arena, it can be configured via config files, in-game menus and console commands.
The most convenient however, less detailed means for configuring the game are the in-game Star Trek: Voyager Elite Force Settings. They already allow for a good deal of customization, especially in terms of key bindings for player character control.
Configuration variables are a more detailed and also more versatile means of configuring EF. They can be set via the console or via configuration files (e.g. hmconfig.cfg). For a comprehensive list of these configuration variables, see Star Trek: Voyager Elite Force Cvars.
For important settings, that might affect your game play, see the Quake 3 Arena article on the subject, or the Net Settings article.