It's actually pretty easy to control as a separate process. If you redirect StandardOut and StandardError then you can subscribe to the Process.OnData* events and receive the command line output. It's then trivial enough to parse the status line using a regex and work out things like % complete and so on.
The hardest thing is working out what command line to pass to get decent quality! I'd recommend this page and this page if you're using H.264/AAC+.