If you get confused about the relationships between IIS virtual directories, applications and pools, use this command:

C:\Windows\System32\inetsrv\appcmd.exe

Voluminous help is available on the iis.net Getting Started page. Useful commands are:

appcmd list site
appcmd list app
appcmd list vdir
appcmd list apppool

The output from these commands can help you find orphaned directories and applications.