With JMS, it uses a single instance of Joomla PHP code to manage the DB.
JMS patches Joomla to allow re-using the same PHP code to connect on the appropriate DB depending on the URL received.
This is explained in the tutorial video 0 (concept)
www.jms2win.com/tutorial#jms12x-0
Each slave site remain indepedent and therefore you have to use the back-end of each slave site to create menu, articles, ....
Only extension that you decide to share can be manage from any slave sites.
Only a limited number of extensions can be shared.
Review product detail.
Here it is the list of extension that are defined in JMS tools and that you can share.
www.jms2win.com/component/content/article/135
JMS does not allow manage the content of each slave site from a central point.
Only the installation of extension can be supervised from the master website.