@DarkSyrius
I have not done the conversion but from what I understand from reading the original post and post #4 by pakrat is the path to the folder for the conversion is: C:\Program Files (x86)\Activision
.... and inside the 'Activision' folder you should have another 2 folders named 'Prototype' and 'Prototype 2' thus allowing each game to be installed in their own corresponding folder.
That's the way I see it and it makes sense but I am sure if I am wrong then either Razor or pakrat will soon correct me.