First, you can not add the master domain name in the manage site. The manage site is used to define the list of slave sites. If you do that, this mean that you want to declare your master as a slave site.
A master website is any website that is not listed in the list of slave sites.
Second, I don't know how to synchronized manually the slave site.
Normally you should have created a slave site in JMS that you deployed in the "public_html".
Becarefull when using the "public_html" when using cPanel. With cPanel, when you create a subdomain or an Addon Domain, the default value is to create them in a subdirectory of "public_html".
If later in JMS you decide to delete the slave site, this will delete the "public_html" directory with all its content.
In the tutorial video 0.b slide 21 to 24, we suggest an architecture to ensure that all the website have their own directory.
www.jms2win.com/en/tutorial#jms12x-0b