Say I have a master site:
- site A (master)
and two slave sites:
- site B (slave)
- site C (slave)

I have 3 templates:
- Blue template (Site A)
- Dark template (Site
- Green template (Site C)
(note: the context of template mentioned here is not the one introduced in jms2win's template for defining a generic rules)

My problem is, when the admin of Site B login into the admin page, he/she are able to change the other two templates (Site Blue & Green).

I understand that under the folder customisation, we can specify each site using a certain themes folder. But there is no complete tutorial to shows how to do it exactly.

In JMS 1.1.x you have 2 methods to create the "templates" directory that depends on the configuration that you did in JMS.
See tutorial CP-05 that show how to have a specific "templates" directory.

So you have to check how the "templates" directory is created in your slave site.
Also you have to tell us if you have deployed the slave site into a specific directory or if you share the master directory.

If you have deployed the slave site into a specific directory (ie. {site_idr} ) and that you have defined a specific themes folder (ie. {site_dir}/templates ) then the result is a creation of a directory "templates" into the {site_dir} and inside you have plenty of symbolic links.
In this case, as explained in the user manual, you can uninstall the themes in a specific slave site and re-install only the one that you want (when you don't want to keep them shared).
In this case, up to you to uninstall the unecessary themes in the site when you don't want to be accessible.

Yea. I've got it now. So I will create a symbolic link to the my master template directory and have the New Themes folder: set to my slave site's directory.

This part I've done. Another problem is about the media. I can see that each of the slave site can see each others uploaded media and able to delete it as well. So how do I overcome it?

The media settings generally correspond to directory "images".
This directory can be specific and show in the tutorial video CP-05.

If your media word correspond to the media directory, you can define a JMS templates where you ask to copy the media directory instead of using a symbolic link.

If you copy the directory, becaurefull that JMS will not update this directory when later you install an extension in the master website that will result by new subdirectories or similar. You will have to synchronize the directory yourself.
The copy could be used when you are sure to now add new extension that would add files inside this "media" directory. Or you could have to syncrhonize it manually.