They have different usages.
Message-Driven Beans and JMS:
Clients do not bind to an MDB like they do for session beans and entity beans. The client only needs to send a JMS message to the queue/topic to which the MDB is configured to listen. Typically clients also use the <resource-ref> and <resource-env-ref> elements of their deployment descriptor and then point to the same JNDI names as the MDB's <connection-factory-name> and <message-driven-destination-name> descriptor elements.
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In ejb-jar.xml, attaching a JMS resource to an MDB requires the <message-driven-destination> entry in the MDB's declaration.