Changes to the database
You can setup MultiSite to execute SQL on each newly created website. Add your custom SQL to 'file/secure/ms_modifications.sql' file. Please have a look at Plugin/MultiSite/files/data.sql to know what kind of data each website hold at the beginning.
E.g. you can add additional permissions for the default website user by adding following line:
INSERT INTO `ip_permission` (`administratorId`, `permission`) VALUES (1, 'PluginName');