Ok, now I understand your problem. So there are basically two options:
1) Expose the jBPM-Console created sessions, so you can interact with them using a remote APIs
2) Let the jBPM-Console use sessions that were created from outside applications, or add the posibility to register custom work item handlers to the sessions created by the jbpm-console.
About 1, there is a way to do that already using Drools Server. But we need to integrate it with the jBPM-console
About 2, I'm 90% sure that you can do it right now.. I've already seen some questions about that, but I don't remember the solution right now.. I probably will take a look on that..
Hope it helps, if you don't find the solution, please report a jira issue with your requirement as a feature request, we will evaluate it and work on it.
Greetings!