I have write How to run PHP in Webmatrix ? few months ago. In this post I will try to explain it little bit better.
When you create a website in webmatrix then try to go to site > settings > here you can find the option for enble the PHP for your website on IIS express.
You can also install the PHP through WPI (web platform installer). The PHP you have installed will be going into C:\Program Files (x86)\IIS Express\PHP/$
$ = version of PHP you have installed.
Try http://forums.iis.net/1166.aspx for any help regarding installing PHP in webmatrix. you can post your idea also to webmatrix.uservoice.com