If you want create fresh slave site with specific "images and templates" folder then you have to create a JMS Template rule in which you put the action = "copy" for the "images and templates" folders (in the folders and files tab).
So that, you will have a new directory structure that will have plenty of symbolic link except for the images and templates folders (as you put the action = copy).
See also the video 0.b slide 31-34 that show the different actions and variant for the template (full sharing, full copy and partial sharing).
www.jms2win.com/en/tutorial#jms12x-0b