As already mentioned by another, I reference this post whenever I need to change the .NET settings for a site.
As for your question, the following steps (summarized from the linked post) should achieve what you need:
Run aspnet_regiis -lk from any .NET framework folder to list your current settings to help you determine which sites should remain using .NET 1.1. If you know there is a .NET 1.1 site, but it is not explicitly listed by this command, then it is inheriting from the root W3SVC/.
For all .NET 1.1 sites not explicitly listed by the previous command, you will need to force them to use .NET 1.1:
Determine the Identifier ID of the site(s) which you want to force to use .NET 1.1. (Through the IIS 6 Manager, you can determine the Identifier of a site by clicking the "Web Sites" folder on the left side of the tool. On the right side, all your sites will be listed, and the Identifier column shows the ID.)
From the .NET 1.1 framework folder, run aspnet_regiis -sn W3SVC//ROOT/ where is the ID of the site which you want to force to use .NET 1.1.
Finally, change the root W3SVC/ to use .NET 2.0 so that all newly created sites will inherit from the root and default to use .NET 2.0. To change the root, from the .NET 2.0 framework folder, run aspnet_regiis -sn W3SVC/.
You can run aspnet_regiis -lk again to verify your settings.
