Daniel van den Tempel har written an interesting article 'Deploying from Development to Public Site'. Is it required to run the 'CMS Manager' on a server that has never had any previous EPiServer installations? Or is it enough to publish the website directly from within V.S. when doing a 'first-time-install'?
Daniels article was discussing how to upload content from your development environment to your live site. The manager still does a lot of setups for you dev. environment. Like creating the project and setting up the database. I guess you could create a new project and add all the references files and folders manually then set up the database and so on but I can't really see why you would want to.