For different JavaEE instance running on same host. Is there a way to have them running with different configuration setting.
Make a copy of the JavaEE directory, call it JavaEE2 or something. And then copy over the config file to the agent-override directory of JavaEE2.
Then from opmn.xml or jserv.properties (whichever is using), for this particular instance, change the location of the bootstrap jar file (etc) to JavaEE2 instead of JavaEE.