You have to check the image, media and template folder fields that you have entered in the JMS slave site.
Becarefull that when you change later the parameters of those fields this may not change anything on the current directory structure that you may have already created.
So if you have not filled those parameters the first time that you have created the slave site, this means that you have requested to share the folders.
You can check the directory structure of the slave site to see if you have symbolic links or real directory.
Concerning the themes (template) directory, as explained in the user manual, event when you specify a directory, this copy the main directory "templates" and create pleinty of symbolic links that you can etiher delete manually or when using the Joomla extension / uninstall template from the slave site where you want to install a specific template.
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