You would have already seen this UI module of mine to set the FTP properties in Active Directory. With IISFtp.vbs not working on WS2008 or Vista, this would be very handy tool to use the FTP AD user isolation. You can very well set the required properties directly on the Active Directory schema yourself, but here is a command line utility to do this.
If you are an administrator who would not use UI stuffs, or you don't want to put on the IIS manager on the server, this one is for you. I created this for one of my customer, and here is this for all.
Hope this helps!