You came to the right place for help but I am not sure I understand your problem.
> I'm not sure if the Java service is pointing to the one I want to add into the package.
The "Java service" drop down box lists the current java projects opened in your workspace, so you can pick the one you want to add to your package. The effect is simply to copy the service's jar file to the /plugins sub-directory of your package.
See the SDK-Tutorial.html doc about packaging and let me know if it doesn't answer your questions.