Problem:

We created our application using the Web Site project template and would like to change to a Web Application.

Solution:

http://msdn.microsoft.com/en-us/library/aa983476(v=vs.100).aspx

Explanation:

Just don't use Web Sites! Why would I want my source code (all of my IP) on a server that could be compromised? They also do not play nice with source control systrems or automated build.