Eclipse is just an IDE. For JMS applications you require a JMS server, which usually is present within an application server, like JBoss. If you are looking at how to deploy JMS applications through Eclipse then they deployed in the form of EARs/JARs. I don't use any IDEs for deploying applications. So i won't be of much help here.
Let us know if you are looking for specific steps to configure and use the IDE to do this. In that case, i will move this topic to our IDEs forum.