There is a function in the menu found in the setup utility under "Tools" called "Convert Website to Web Application". With this the setup will try to convert an existing website to a web application. This involves adding .designer files and creating a suitable project file. Make sure you update the site to the latest version first. (You will get a warning if you do not.)
The conversion is not always 100%, and it is likely you will need to make some manual changes to the project afterwards before it compiles, but it should save you a lot of time. Unlike websites, web application projects requires that every public class has a unique name, this includes page classes found in code behind files of aspx files. Quite often you will need to rename some of the page classes, but that's about it.
PS: We've also added support for MVC applications, but there is no automatic conversion here. To get going with MVC start with the new MVC example application found in the setup utility.
Ole