With VS.NET 2005 all virtual directories inside a web application as assumed to be part of the ASP.NET project. This causes some problems when building the project as all files in the "CMS" virtual directory are included in the compile. As these files are only stub files for the code included in the MCMS binary files the compile of these files is not required and also could cause problems.
Spencer shows how to use Web Application Projects (which are currently in beta) to overcome this limitation. Web Application Projects give developers the same ability to create projects as with VS.NET 2002 and 2003 possible.
See here for Spencers article: http://www.mcmsfaq.com/articles/sp2wap.asp
Caveat: using Web Application Projects for MCMS projects in not a supported solution. So if you would have problems with this approach you could not expect to get support from Microsoft.