The source is being expanded in a version dependant directory under /opt, e.g. /opt/znuny-6.0.37.
A symlink is used to point to that then, e.g. /opt/otrs -> /opt/znuny-6.0.37. That symlink is updated at every upgrade.
The primary configuration file is /opt/otrs/Kernel/Config.pm
Configuration can be done either via the Web interface or by changing Kernel/Config.pm and shipping the change via puppet. The file overrides whatever changes happen via the Web Interface. When you change the config, reload apache to clear the mod_perl cache.
Znuny configuration is meant to be primarily done via the Web interface. Stick to that for most use cases.