In order to debug through your plugin you will need to attach your eclipse to a running Jive Messenger. I am not sure, but I don’'t think the default installation is built with debugging info, so the easiest way to do this is to have the actual messenger source. Then you can attach to it or maybe even launch from eclipse. There were a few threads about that already if you have a search you may find it.
As Ryan mentioned, using JM build script you can also build and deploy you plugin.
rename build\build.properties.template to build.properties
add the location of your plugin dir to the entry “plugin.dev.dir=” as per the instruction
Then only other thing I can suggest is that you try to keep code that is independant of Jive Messenger in seperate class(es), so you can test your code outside of a running messenger. You can even write unit tests for them. If I may suggest you have a look at the content filter (plug!) src, the actual message filtering is done in a seperate class so I could unit test it outside of Jive Messenger.
Hope that helps,