When you enter a battlefield, be it land, mind or disk, be aware (wink):
"No plan survives contact with the enemy"
-Helmuth von Moltke the Elder
That's not to say you should have no plan though. Quite the contrary:
"Victorious warriors win first and then go to war, while defeated warriors go to war first and then seek to win."
-Sun Tzu
When it comes to working with .NET on the web you have a lot of flexibility on how you approach a project. One particular aspect which seems to be a constant point of contention is the differences between Visual Studio's Website (WS) and Visual Studio's Web Application project (WAP). I had to work with both and over a long time and lot of arguments I learned quite a bit about the differences. Almost anyone who has written an article about this will tell you that you can accomplish pretty much any task with either approach and that choosing one over the other really comes down to your preference and situation. I started working on the WS model and have found that it is suitable for some tasks but the longer I develop the more I find myself using the WAP model because the environment and tools it offers tends to help me accomplish my goals faster and with more precision. It should also be noted that both project types are still reliant on IIS and the model type you choose really only changes the way you work with the project, not how IIS views the files. It's more a difference in the paradigm the two offer.