From VS.Net 2003 to VS.Net 2005
The first problem I face is:
What is the difference bwtween WebSite and Web Application?
I read the article that Web Applicaion emulates the environment like Web Project in VS.NET 2003,
but I could not see why I should use it.

Any advice would be very appreciated.

Take a look at: http://west-wind.com/weblog/posts/5601.aspx  It should help answer your question.