If you want to share the same joomla "/templates" directory for all the websites, you can do that when you specify the action="special copy" in the JMS Template.
In this case, this create a Symbolic Link on the "/templates" directory.
As both your slave sites have their own templates directory, perhaps you should have to copy (merge) their files into the master website /templates directory before creating a link to this directory.
JMS will not update current "/templates" directory.
So before reapply the JMS template modification on the slave site (open and resave the slae to apply), you will have to rename the existing "/templates" directory of your slave site just to be able restore it very quiccly in case of problem.
If you have correctly prepared the "/templates" directory in your master with all the content currently present in your slave templates, theorically, this will be replaced by the link with the same content and therefore available for all your website.
If you want that we assist you in this operation, we can do it with our billable support that you can order at
www.jms2win.com/download?page=shop.produ...35&category_id=1