If you have the old Atlas CTP installed and want to install the new CTP you will need to uninstall the old Atlas Template file. If you don't when you select File->New Website in Visual Studio 2005 it will look something like this:

To remove an old template file you need to go to your project template location and delete the template.

To find out where your project templates are stored go to Tools->Options->Projects and Solutions and click General. Your template files are located under the Visual Studio User Project Templates location.

Once you go to the templates location just delete the appropriate zip file and you can install the new Atlas CTP without messing up your My Templates screen.