To shutdown the different instances:
Execute the shutdown.bat or shutdown.sh script from the /bin directory with 2 extra arguments. The first argument is the hostname and the second is the port number.
Example: If you have configured 2 instances of JBoss, one on port 11099 (the NamingService port) and another on 11199, then in oreder to shutdown the first JBoss instance use this command:
<jboss_home>\bin\shutdown.bat -s jnp://localhost:11099 -u <username> -p <password>
And for the second instance , use this command:
<jboss_home>\bin\shutdown.bat -s jnp://localhost:11199 -u <username> -p <password>
Note: The port will be each binding port that was specified for jboss:service=Naming
Note: UNIX users use shutdown.sh.