This page might be of some help: http://ez.no/developer/ez_publish_3/documentation/installation_and_configuration/configuration/configuration_files
The override.ini (+ .append files) are used to configure which templates override which ones. The overriding templates are in override/templates under a design.
The site.ini (+ .append files) are used to configure site settings.
- .append files append settings to a configuration file in /settings. - the "override" folder in /settings is used to store the site-wide .append files, and is not related to the template override system.