This solution works for me when I needed to force two diferent versions of PHP on a Windows Server 2012 r2 & IIS:
For one application, map *.php extension to a CgiModule adding the "-c" option to the executable path, like this: "C:\php53\php-cgi.exe -c C:\php53\php.ini"
For the other application, map *.php extension to a CgiModule adding the "-c" option to the executable path, like this: "C:\php54\php-cgi.exe -c C:\php54\php.ini"
I think that way is the cleanest, because there is no need to work with PATH variable or Registry or Windows directory.
Note: for some reason, this didn't work on FastCGI module, related to the way that IIS set the executable tab not allowing command line options.