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.
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'?