website or a web project is different from web application. Show all files, copy local to true these option are not there in web site. When you add a reference to your project. The dll will be automatically copied to your physicall directory. It implies it is working as if you have set copy local = true in a web application. It also implies that your project is a stand alone, if something is changed outside your project say a function in your referred dll is taking more input parameters, your project will not be affected. Suppose if the referring dll is changed and you want the new version.You can expand the bin then your dll. there is one more file called refresh you can make use of it.
There is service pack in 2005 if you install it you will be able to create web apps. Web apps have lots of options, it will automatically create the virtual directory in IIS.these things are not in website