What might happen is that you can only use one port for the primary display, so if you pug it into the other one you will get a black screen or something. I had to use the one on my right (looking at the tower from the front), but in my case they are both DVI. I don't know if modifying some com.apple.boot.plist injection could switch the "ports assigned to your primary monitor". I know there are different values for VGA/VGA DVI/DVI VGA/DVI and DVI/VGA, but I'm not sure it you can change them and still keep your card working with OS X.