By default cgi stuff is enabled by default (thats where all the security holes come from)
IIS really does not care where the cgi folder is placed as long the IIS has access and the Web pages now where it is.
But by default it is something like this
c:\Inetpub\scripts
Now are you going to do Script mapping like (ASP, PHP, or Foxweb) where you use ISAPI or are you going to do it the UNIX way and call the Engine in the URL?