My simple answer for this complex question is that use events. Build your workflow in a way that it is waiting for events (you can set your workflow tasks to wait for these events). Trigger these events from your web dynpro. This is the best practice in most cases in workflow development.
Try to "separate" the workflow and web dynpro component(s) from each other. Just trigger events from the web dynpro (you don't need to know anything about the workflow in your web dynpro component).
Kind regards,
Karri