When you want to create a sub-domain like
slave1.mydomain.com you have to defined it into the CPanel and specify the directory of your master website.
If you let CPanel create the sub-domain into a specific directory, you will have to specify in JMS the deploy directory of your sub-domain path provided by your CPanel.
When this is the master directory, the JMS deploy directory must be empty.
When you want to create a slave site with a specific sub-directory like
mydomain.com/slave1, you have to create the slave1 directory manually and when the directory exists, specify in JMS the full path to this directory. ie. {root}/slave1