Following is the article that stats steps to convert a web site project to web application project. http://webproject.scottgu.com/CSharp/Migration2/Migration2.aspx
During migration, it will be changes in the project structure and additional files will be created (.designer). App_code files will be moved to Old_App_Code folder and there will be one assembly file for complete project. One assembly will restrict our flexibility to use C# code along with VB.NET because .NET cannot compile multiple languages into one assembly.