To perform a clean install of Windows into a directory other than winnt (default), without having to perform a parallel install, use an answer file or other time-consuming methods, just create a set of bootup disks (4) for Windows 2000 Server.
On disk 1, open the file "txtsetup.sif", and search for the entry "defaultpath=winnt". Modify this path so it reads "defaultpath=wtsrv" or whatever you would like the default to be.
I use this method when setting up terminal servers, as it then allows me to query the %windir% variable & identify customers that are logging in via WTS. This way I can branch out & not execute SMS, anti-virus, etc. commands for such customers.