You either decide to create domain or subdomain with specific directory (and therefore use JMS deploy directory in those directories)
OR you decide to have all the website (domain and subdomain) in the same root directory than the master website (not in another directory).

If you want to create another direcrtory, you can do it manually with a SSH where you create a link between this specific directory and the master website root directory.

If the directory where you want to deploy the slave site is the parent directory of the master directory, this will be difficult to create a link between the parent and its children.

If you want to create the following structure, you will have a problem:

(slave domain and slave sudomain) = /home/domain/
(Master website) = /home/domain/master

If is not possible to define the '/home/domain' as a link to '/home/domain/master' as by definition /home/domain does not exisits.

OK thats clear info!