You will find system-wide defaults in this file

/usr/local/topicdesk/roundcube/WebApp/config/main.inc.php 

For example, to change the help link in Roundcube, change:

$rcmail_config['support_url'] = "http://help.wherever.com/"; 

Its important to note

User default settings established for a user when they first login. Once the user has logged in, they are in control of their settings (now stored in the database). Changing a default user setting has no effect on existing users.

If you would ever like to start from scratch, the database can be re-initialized and all users will start with default settings.