In the version of Visual Studio 2012 I am using (downloaded at the end of the Release Candidate phase), I can only access the Website Administration Tool in the Website menu in the menu bar at the top, under the command 'ASP.NET Configuration'. The Website menu was only available if I selected the website or one of its content files or folders in Solution Explorer.
By contrast, if I selected the solution in Solution Explorer, the Project menu becomes visible instead of the Website menu, and the ASP.NET Configuration command is NOT available there.
Contact me for screenshots if desired. I have them, but as a newer user, they did not allow me to post them.