No one can really help you with your specific app, because no was has any idea what your app is doing. I have a Spring/Struts based web application, and I simply integrate the jbpm libraries. How to do this is covered in the documentation, I think under the deployment section.
To get ideas how to use the the API's, you can look at the source code for the jbpm console, and examples also found in the documentation.
I would recommend reading the docs, looking at the source code, and researching on wiki and forums.