Ok, I have PHP running on IIS here at work and I have doc_root left blank.
Firstly, are you using a windows server (as in, multiple websites on the server, not just multiple VDs)? If you are, then you can set up each "website" how you want (i.e. some can run PHP stuff and some can't)
Also, have you set up the properties of the webserver right, so it can actually make use of PHP?
If you haven't then go to the properties of the "website", then click on the "Home Directory" tab, click "Configuration", then "Add". In the "Executable" box, you can either browse to the php.exe file, or just type it in if you know the path and in the "Extension" box simply type ".php" (or whatever extension you want).
Finally, restart the "website" (not the webserver itself) and bob's your uncle.
Hope this helps.