You can use the approach similar to the one described in this article http://learn.iis.net/page.aspx/208/#Per-site (look for the section "Per-site PHP process pools")
The configuration will looks similar to this:
<fastCgi>
<application fullPath="C:\PHP\php-cgi.exe" arguments="-d my.website=site1" activityTimeout="<value1>" />
<application fullPath="C:\PHP\php-cgi.exe" arguments="-d my.website=site2" activityTimeout="<value2>" />
</fastCgi>
The for each web site define a handler mapping for PHP as below:
Site1:
<system.webServer>
<handlers accessPolicy="Read, Script">
<add name="PHP via FastCGI" path="*.php" verb="*" modules="FastCgiModule" scriptProcessor="C:\PHP\php-cgi.exe|-d my.website=site1" resourceType="Unspecified" requireAccess="Script" />
</handlers>
</system.webServer>
Site 2:
<system.webServer>
<handlers accessPolicy="Read, Script">
<add name="PHP via FastCGI" path="*.php" verb="*" modules="FastCgiModule" scriptProcessor="C:\PHP\php-cgi.exe|-d my.website=site2" resourceType="Unspecified" requireAccess="Script" />
</handlers>
</system.webServer>