Running version 2.0 of the .NET Framework does not seem to be too complicated. Note however that there is a separate version of the Framework for 32 bit and 64 bit versions. Another thing of importance is that IIS will only run in either 32 bit mode or 64 bit mode, not both at the same time. Microsoft has an article detailing how to switch the mode IIS uses here.

Version 1.1 of the Framework, on the other hand, can be a bit confusing. Unlike version 2.0 of the Framework there is not a separate version for version 1.1, both 32 bit and 64 bit versions use the same setup file. Another restriction of version 1.1 is that IIS must be set to operate in 32 bit mode, so if any other websites using version 2.0 of the framework are running on the server, they must be compiled to work in 32 bit. I had problems installing the Framework from the setup file. I received an error about not having sufficient disk space. More about this and a solution can be found here.

Why is the ASP.NET tab missing from the property pages of website in IIS? Good question, ask Microsoft. This seems to be a bug in the 64 bit version of Windows. When versions 1.1 and 2.0 of the Framework are installed, the ASP.NET tab which would normally be visible and allow you to switch the version the application will run under, is missing. There are a few workarounds. The first is a manual fix for the websites that need to be switched. Under the application configuration settings, on the mappings tab, change each extension to point to the correct aspnet_isapi.dll location. There is an aspnet_isapi.dll for each version of the .NET Framework installed, by default, in the "WINDOWS\Microsoft.NET\Framework" folder. If the current version is 1.1 and you want it to run under 2.0 you would change the location of the aspnet_isapi.dll from "WINDOWS\Microsoft.NET\Framework\v1.1.4322\aspnet_isapi.dll" to "WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll". Another option is to run the aspnet_regiis.exe file with the appropriate switches to configure the correct website and/or virtual directories. I have not undertaken this approach, but it is possible. This brings me to the last method which I will list. A handy program to change the ASP.NET version used by IIS can be gotten from Denis Bauer. It can be downloaded from his site here. He basically runs the aspnet_regiis.exe inside of his application to do the configuration. More info can be found on his site.