How Jython can be used in Eclipse is described here: http://jydt.sourceforge.net/
Bad news:
This is not supported yet, although mentioned as desirable by the users of JyDT:
* Java projects as referenced projects of Jython projects
* Navigation to Java code
* Debugger for Jython with integration with Java
* Show inheritance relationships between Java and Jython classes
* Using compiled Jython classes in Java projects