Visual Studio allows the creation of a new project type call Web Application Project. This is different from the standard ASP.NET web site project. The WAP is based more on the application model of setup. Class and component files can be added anywhere within the project and they will be compiled normally.

For more information on converting your 2005 web site to a WAP site visit http://msdn2.microsoft.com/en-us/library/aa983456.aspx.