Usually programs like those have a configuration file on the system, usually clear-text, so you can edit it with a text editor of your choice, just remember the file syntax. Most configuration files should be somewhere under /etc (system-wide configurations), or under your home directory in a directory that starts with a dot like /home/username/.gnome2/ (per-user configuration).
Some config files even have their own manpage that describes what and how you can configure the program. That manpage may be named after the program itself, or in some cases the configfile. Try
for example, and if you find something interesting, like for example "/etc/snort.conf" (that was off the top of my head, probably not real), you then use
Code:
man /etc/snort.conf
to see that man-page. If nothing else, you use
If the program runs as a service (i.e. is always running or automatically started) you'll often have to restart the service or force it to re-read it's configuration after you've changed it.