When deploying to IIS you should use port 80, or port 443 if using SSL. We use port 9009 in DevForce almost as a legacy: if you deploy the BOS as a console or Windows service you need to assign a port, and 9009 seemed like a good default. In the n-tier and Silverlight templates we continued setting 9009 as a default, but I want to emphasize it is not in any way a DevForce requirement that you use this port. In IIS you can't use it, and non-IIS deployments aren't that common in DevForce 2010.
The *.svc files - you do not need them if you've registered a VirtualPathProvider in the global.asax. If your global.asax is the standard one from our templates or samples then the registration will be done. If you keep the .svc files you need to make sure they contain the correct information (which you can find in our Deployment samples). It's far easier to just remove the .svc files altogether.
The Type conflict error - the first EntityManager created by default becomes the DefaultManager. You can also explicitly set the DefaultManager. On the server side you should NEVER use the DefaultManager, since that would mean you're sharing the EM among threads. If you see the error on the client that means that "something" already created a non-subtyped EntityManager. If you're using the new Business Application templates, that "something" would be the AuthenticationManager, which uses an EntityManager for login processing. If you're not using the BAT, then it's hard to say what happened. To fix the problem, explicitly set the DefaultManager to your sub-typed EM first thing in your code.