Hi Ian
If you changed the settings via the theme through the appearance settings these will be applied at the site level.
The blocks appear on different levels - the Frontpage and Dashboard blocks will be applied to the site.
Blocks on courses will apply to the course only - it is possible to change the default blocks for new courses by editing the config.db file - this is documented in the config.dist file that comes with Totara or you can use a backup and restore for a course so the appearance of the courses are the same.
Regards