Do you mean two different versions of PHP ie.e 4,2,1 & 4.1.1? Or are you asking about CGI vs. ISAPI in PHP.
I run a website with IIS 5 and PHP 4.2.1 (no asp). I use ISAPI. It is a very very active site with 20,000+ unique visits. ISAPI has had no problems at all. CGI seemed to want to bog down under high use.
If you use the ISAPI version of PHP, do not run the Windows installer at all! Simply place php in the c😛HP directory and the php.ini in the c:winnt directory. Open your MMC and add a php extension parsed with c:\php\sapi\php4isapi.dll. Then go add an isapi filter called php pointing to the same dll. Stop and start the service. Make sure your ini file is pointing to the right extensions directory and the path is correct to your session data folder. If you have already ran the CGI installer, the ISAPI may not run, I had to format and re-install to switch to ISAPI. There might have been an easier way, but this is all I knew.
If you plan on using the cgi version, run the installer.
If you want to use two different version numbers of PHP, yu will have to manage 2 different php.ini files in the winnt directory and place the second version number in c:\php2 directory.
I hope that helps.