To debug your program, choose Run|Debug. If necessary, your code is re-compiled. When debugging, you can view information about threads and data values, and you can step through your source code. You can debug both local and distributed applications, including servlets, JSPs, applets, EJBs, unit tests, and applications.
For more information, see:
Building Applications with JBuilder: Debugging Java programs
Distributed Application Developer's Guide: Debugging distributed applications