A good place to start is by identifying a single path through the application, take the addition of some item to the database.
If you start the application up through Eclipse then set a breakpoint in the Hibernate DAO or domain object that is used for that. Run through a typical user interaction for the additiuon of that item, once you've hit the breakpoint then work backwards (via the call chain) until you reach the user interface. You should by now have identified a complete path through the application and the main components involved. Alternatively, if you know the main user interface component from which that begins (Servlet or otherwise) then you can start from there and step through each method call.
It's important to make notes of the main classes involved in this interaction, either pen and paper or you can document it using UML - use a sequence diagram.
By the way, if you can't start your application through Eclipse then attach a remote debugger to the application server/servlet container that your application runs in.
e.g. For Tomcat see http://confluence.sakaiproject.org/display/BOOT/Setting+Up+Tomcat+For+Remote+Debugging
That's one method that can be used for understanding the workflow.