How do I talk to my TransportAgent?

Question

So I have my TransportAgent (sort of) working. How do I talk to it to configure it? And I need to allow individual users to make settings for their account (like an anti-virus being given a white-list for a specific user). I need this for Exchange 2007/2010/2013 so I assume EWS is out. I would like to have:

1. I can write an Outlook AddIn that communicates including the user identification so I know who to set things for.
2. A web page that provides the same (part of the web mail_server/owa web page is fine).
3. A means for administrators to set both system config and individual user settings. Using whatever means for the U.I. that is standard.

Also, is there a good book out there that covers all of writing TransportAgents, including questions like these?