Yes you can install JMS after that you have setup a website.
In general, we recommend to put JMS on an empty website and consider the master as a repository where all the extension will be installed and without any content.
After create the first "public" website.
Concerning the directory structure, we published in the "tutorial video 0.b" but also in the different power point of joomla day and Joomla World Conference the recommended directory structure depending on the website type (domain or subdomaain or subdirectory).
To avoid that search engine detect a website as a subdirectory of another one, we recommand a directory naming convention like
domains/DOMAIN1.COM/public_html
domains/DOMAIN1.COM/subdomains/SUBDOMAIN1/public_html
So that each domain or subdomain have their own directory that is never a subdirectory of a public thing.
You can create website like mysite.com/site1 but in this case, all the websites will be saw from the mysite.com
I hope this will help you
See also
www.jms2win.com/en/tutorial#jms12x-0b
www.jms2win.com/en/documentation/doc_det...-day-strasbourg-2012