Create <domain-dir>/domain/example.com
Copy <domain-dir>/domain/en/i18n.properties to <domain-dir>/domain/example.com/en. This would be the default path of the i18n.properties for users in example.com domain.
Create directories for each supported locale such as en_US, ja, de_FR under that domain, copy i18n.properties to the domain, and change the locations accordingly