First you need to decide on the provider for JMS. It could be WebSphere MQ, the JMS provider that comes inbuilt with WAS or some other provider too.
Refer to the redbooks https://www.redbooks.ibm.com/Redbooks.nsf/RedbookAbstracts/sg247770.html?Open.
- You can use InitialContext to lookup connection factory and Destination.
- You can deploy the JMS app just like any other app. But ensure that JNDI objects are configured.
This is also a nice info-center to use for reference: http://pic.dhe.ibm.com/infocenter/prodconn/v1r0m0/topic/com.ibm.scenarios.wmqwasusing.doc/topics/scenario_overview.htm