You have the option of linking both card together or seperate in precision X. I believe it'd the same in afterburner.
I've tried unlinking in precision X a week ago and it didn't work. Whatever settings I set it did for both cards. Maybe it works for older cards or maybe cards not runing in sli.
I used to always use afterburner but this time I like precision X since I understand it now. Back when was hard to find what I was looking for.
Though I can't get it to load with Windows even though I have it set to load on boot up. I always have to wait for Windows to finish loading and then open it.. hopefully it works right when I install win10 pro fresh this time.
Currently stuck on the phone till I finish building the new rig. :/