First if you test JMS on a localhost, there is a special procedure described in the user manual that explain how to simulate a domain name.
If you want to create a slave site with
mydomain.com/subsite, you just have to deploy the website in this directory and perhaps ask to create the directory.
In JMS, you can also ask to create the directory when not present.
For example
Site ID = slave1
domain = {site_url}/{site_id}
deploy directory = {root}/{site_id}
Create directory = ON (Enabled)
Becarefull that when you do that without a JMS templates, this will also create symbolic links in each new slave site with the exting directories.
Perhaps it would be better to create a JMS templates rules to specify which "Files and Folders" you want to create for the slave site.