If you have JBuilder Enterprise Edition you should be able to debug remotely. Search the forums for JBuilder and debug - someone has answered how to do that already.
If you could only afford the standard edition (like me) you can debug your code by running all of JBoss in a debug session. This would be really horrible to do, except someone has written a JBuilder wizard to do all the hard work for you, and it can be found at:
(this link is for JBuilder 7, but go to the site given on that page and they have stuff for other versions.)