While it is completely unsupported by Microsoft, I ran into a few issues dealing with IIS and ASP.NET projects in Visual Studio 2003 along with Visual Studio 2005. Note that through all of this (and in general) I run with UAC turned off.
First off, it's required that the IIS6 Compatibility Layer be installed otherwise none of this will work.
After installing both VS2003 andd VS2005 (in that order), I was unable to install anything dealing with IIS from the "Programs and Features" control panel. After several hours of trying various things, I finally found the solution. I had to uninstall the .NET Framework v1.1, after which I could install any of the IIS options available to me.
I then re-installed .NET Framework v1.1 and ran into the second issue. Every time I attempted to open an ASP.NET 2.0 project, it would ask me if I wanted to configure the server to use ASP.NET 2.0, even though the application directory was already setup to do so.