The installation program for ArcGIS Server for the Microsoft .NET Framework and the AddInstance utility, located under \ArcGIS\DotNet, is designed to only setup and configure an ArcGIS Server Instance, which includes the ArcGIS Server Manager application, on the default Internet Information Server (IIS) Web site.
This situation is due to two limitations of IIS:
1) IIS only stores the physical location of the default Web site in the registry, so other Web sites are not maintained in a searchable repository.
2) Changing the default Web site root folder, also known as the 'Local Path' property, in IIS Manager does not update the registry.
The documents listed below describe three common scenarios for configuring an instance of ArcGIS Server Manager on a non-default IIS Web site.