Your last sentence is not clear.
If you mean that you define a slave site with exactly the same domain than the master one then in this case, this mean that you will convert the master into a slave and that you will need another domain or subdomain to access your master.
In other words.
If your master is
www.domain.com
Then if you define a slave site with domain =
www.domain.com then this will convert the master in a slave.
I remember that when a URL is received, JMS Multisites starts to check amoung the list of domain defined is there is a match with a slave. If YES then this is a slave.
Otherwise (not match) this is the master (the default).