The site is the root and there is a /Forum.aspx page in there which contains the forum user control. All of the YAF files sit withing a yaf folder which sits within the website root. This is not configured as a virtual directory in IIS. The webroot also has all of the necessary config files in order to run yaf.
ie
www/forum.aspx (this contains the forum user control)
www/yaf/(all yaf files here)
Let me know if you need more info.
Thanks
Kev