you can tell by the bios switch on the side of the card, slide the switch to the left and that is your primary bios slide the switch to the right and that is your secondary :)
as far as i can gather it shouldn't matter how many cards you have in the machine it just looks to update all of them, i would maybe disable SLi but if anyone else would like to chip in, go for it
update on Primary first then reboot to check and see you did it right then move the switch to the right then update the secondary, reboot to check. switch bios back to primary and happy days