In your IIS properties for each site, go to home tab and click configuration, then map the script maps for that site to the version of php you want it to use. WARNING if you use the default worker process thread and two sites or more are using the same version of php, and one site crashes php, well guess what (see I knew u were smart..)
BTW.. with ISAPI, you need to restart IIS to reload the php.ini values, unlike the cgi executable version which inits on each call..
Your best to run each site in there own worker process accounts, and this is way better handled in IIS 6
Have phun ;