Like explained in the tutorial video 0.a but also in video 0.b slide 10, the concept of JMS Multisites is to share the same joomla installation (PHP code).
One of the solution to share the same Joomla php code is to use Symbolic Link.
So when you deploy a slave site into a specific directory, JMS Multisites create plenty of Symbolic Link to your physical joomla installation.
You can control the link with the JMS Template menu and when you define rule.
See also the tutorial video 0.b slide 31-34 that give more detail on the way to create a rule for the new directory structure and symbolic links.
www.jms2win.com/en/tutorial#jms12x-0b