ameh stores its configuration in a file like this:
[jira]
install = /opt/atlassian/jira
home = /var/atlassian/application-data/jira-home
classes = %(install)s/atlassian-jira/WEB-INF/classes
crowd = %(classes)s/crowd.properties
db = %(home)s/dbconfig.xml
[confluence]
install = /opt/atlassian/confluence
home = /var/atlassian/application-data/confluence-home
db = %(home)s/confluence.cfg.xml
# Any apps you don't use will have their sections commented out
#[crowd]
#[fisheye]
New configuration settings can be added using the ameh command-line, or by directly editing the configuration file (which will typically live in /etc/ameh.ini).