My master is installed at master.domain.com, JMS is installed here. My homepage is at domain.com.

However when I got to backend of domain.com it's a replicate of the master. JMS shows up here too. It is using the same database and even says master in site title. So I am trying to delete the replicate but I can't find it.

In cpanel I notice I have a public_html/master folder and there is a bunch of sub folders. One of the folders is master, so it's public_html/master/master. Inside that folder it duplicates the master. SO a folder inside a folder with the same info. I'm guessing one is the real master and the other is the replicate. How do I know which is correct so I don't delete the correct master?

If your "domain.com" display the master.domain.com, this is perhaps the symptom that the slave site "domain.com" is not correctly defined in JMS.
When a domain is not defined in JMS, it automatically display the master website content.

When you mention the "/public_html/master" that includes again master, ... master that let me suppose this is not a directory by a symbolic link on the master that itself contain the master directory.

In fact, I imagine that your master website is in fact the "/public_html" and that the "master" subfolder would be a directory that would have created to build a slave site called "master".

Normally, when you follow our recommendation present in tutorial video 0.b, you should put your master beside everything.

As I don't know which is the real master (public_html) or the subfolder master, I can just tell you to be very carefull before deleting something.
If in fact your slave "domain.com" is located in the upper directory of your master (here public_htmk), if you request to delete this directory, you will also delete the subfolder master that would be the real master.

If you want that we have a look into you specific configuration, this is possible with our billable support that you can order at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1