As explained in the tutorial video CP-05, most of the templates or extensions does not use the Global Configuration "media settings" and the JPATH_THEMES defined present in Joomla. In general, they hardcode /images and /templates.
When this is the case, that means that you must have website that keep this directory structure and you can not modify the path.
That mean that you must configure your doman or subdomain in your HTTP Server to have specific root document directory.
In this case, you have to put in JMS the deploy directory = to the specific root document directory that you have specified in your HTTP Server.
If you want that the slave site be able to have a specific (themes) /templates directory where it can install additional templates then see tutorial video 0.b slide 34
action = special copy
Themes folder = {deploy_dir}/templates.
As each domain or subdomain have not a speciifc directory, you can just use in JMS template images folder action = copy
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