About the jndi-URL it should be jndi-URL="jnp://127.0.0.1:1099", so you can include the port. Your other question puzzels me a bit because the whole idea of having JBossESB is to have the opportunity to have multiple .esb in your deployment. You can define a connection with your JMS server just by the following code:
or if you want transacted JMS (-JCA)
Are you experiencing some trouble when you deploy more then one .esb?