Your web project will have a project file, and it will build into a single dll in the \bin folder. This opens many doors and IMHO addresses many problems presented by the new compilation model introduced with VS 2005 Web Site Projects. There are a ton of great features that come along with this too.
Ever since I posted this entry back in November 2005, I've grown more and more frustrated with the new compilation model introduced with VS 2005. And I had come to realize that my current project had virtually zero chance of migrating to ASP.NET 2.0, which made me very sad. But the Web Application Project model allowed with this add-in makes this much more feasible.
This blog entry is definitely worth a thorough reading for anyone doing any heavy lifting in ASP.NET, 1.x or 2.0.