If you want to copy the "/template" directory, you can create a JMS template (menu) and in the "files and folder" tab, use the action "copy" beside the "templates" directory.
Review potentially the other directories.
When you have save the JMS templates (ie. template id = duplic_templates_dir) the you can create a slave site that use the rule "duplic_templates_dir".
When you go in JMS manage site, select the JMS templates that you have created.
In a JMS templates, you can setup all the default values you want to avoid enter them in the manage site. This also allow you to change the default JMS behavior when it creates a slave site.
If you want that we setup your environment, we also have billable support that can be ordered at
www.jms2win.com/download?page=shop.produ...35&category_id=1