The jbpm-server (or jbpm-gwt-server) expose a rest api to be called to interact with the engine. The console is using that server to interact, so if you use that service all the changes will appear in the console. If you embed the engine in you application you will need to find the way to notify the console about the changes.. probably making that your server installation look for the same database than the one that is using your application.
Cheers