The concept of JMS is to share the same joomla application (php code) between all the websites and continue to have specific database (or at least specific table prefix) for each website so that their content is specific.
For a limited number of extension, it is also possible to share the content present in the DB.
www.jms2win.com/en/list-of-extensions?vi...id=269&Itemid=53
It is effectivelly possible to share the joomla users (and VM users) between the different websites.
This case is illustrated in the tutorial video 16
www.jms2win.com/en/tutorial#jms12x-16
Concerning VM2, if you share its content, this will mean that all the websites will have the same products with the same prices. Default shopper group could be used to have different prices but have different default shopper group depending on the website is not something that exists in standard.
So I suppose that you should keep the VM2 content specific for each website (except the users that will be shared).
Concerning the templates, the joomla "/templates" directory can either be shared or specific for each website.
Concerning the VM2 layouts if they are stored in the /components/com_virtuemart/views/virtuemart directory, they will be shared by all the website.
Normaly, when creating a specific layout for VM2, it would be better to implement it inside the joomla /templates directory