Perhaps you could have a look in the tutorial video CP-05 that show how to have a specific templates directory.
See also the tutorial video 0.b - slide 34 that show the different variant to share the templates directory, share partially the template director or simply have a copy of the tempalte directory.
www.jms2win.com/tutorial#jms12x-CP-05
www.jms2win.com/tutorial#jms12x-0b
A basic website creation is show in the tutorial video 9 or CP-04.
www.jms2win.com/tutorial#jms12x-9
www.jms2win.com/tutorial#jms12x-CP-04
Concerning the sharing of the menu, it is only possible to share the menu item (not the full menu). This is what the "Multisites Menu Item" is doing.
If you follow the tutorial video step by step, this should give you a better understanding on how JMS Multisites is working