If you want to replicate the master website to build a slave site with the same content, you can have a look in the tutorial video 0.d (moreless at the middle).
We show a JMS Templates rule called "replicMaster".
You can also find in the forum several description of the "ReplicMaster" rule.
www.jms2win.com/en/forum/24-joomla-multi...-before-i-begin#8381
If you want to replicate a slave site to build a clone of slave site, you have similar thing with the tutorial video 16 that show how to replicate a slave site and also sharing the users.
All these example show a replication of an existing website and therefore avoid to have a fresh Joomla installation
You have a fresh Joomla installation because in the JMS template rule, you didn't have specified a website to replicate.