Seting up IIS5.0

after you install iis you can click the copmputer in the mmc console of iis and select the default website. right click and select properities and go to the home directory tab. change the location from c:\ to d:\ or where ever and all the files strand for iis will be copied. I would recomend using the microsoft iis lockdown tool.

here is the link:
http://www.microsoft.com/windows2000/downloads/recommended/iislockdown/default.asp

hope this gets you in the right direction. the tool is wonderful. install ftp and wwroot different directories is not nessary but moving iis from the c: partition is always a good idea

Here is the "official" word from Microsoft:

Cannot Install Internet Information Server Using Optional Path in Windows 2000 (Q244852)

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The information in this article applies to:

Microsoft Windows 2000 , Server

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SYMPTOMS
When you install Microsoft Internet Information Services (IIS) as an optional component of Microsoft Windows 2000 Server, you cannot designate a path that is different from the path of the default IIS installation folder.

STATUS
Microsoft has confirmed this to be a problem in Microsoft Windows 2000 Server.

This is just how it works. The previous answer, which explained how to change the directory for the Default Web Site, is correct. You can't set wwwroot anywhere else on install other than ROOTDRIVE:\inetpub\wwwroot