You can use MantaRay in two ways:
1) As part of your POJO (plain old java objects) application, in this case you do not need a JNDI you just import and use the MantaRay JMS implementation. You can take a look at one of our examples in order to better understand how you can do it.
2) Under J2EE application server, in this case the MantaRay will replace the MOM in the application server
If you want to hook MantaRay to an application server - you will probably need a JNDI, because - when working with MDB's - they look for their connection factories and destinations in JNDI. You can't really get around it.
As for why would you want to use MantaRay when you already have an application server - the question is the other way around - why use an application server if you got MantaRay ;-)-. When comparing MantaRay to other JMS providers (even those residing within an application server), you quickly come to the conclusion that MantaRay has better throughput AND there is no need for JNDI on the clients (the application server may need it for MDBs but the stand-alone clients don't need to do anything with JNDI). If you're going to use an application server - you have to go by its rules - if you want it to function in the way it is supposed to.