Please anyone feel free to correct me, but as far as i remember, you have to close all your overclock tools first (MSI afterburner, nvidia-smi, etc) then run the pill first and then run your mining software second. After those are both running smoothly, thats when you open your overclock tools and apply settings. The settings won't be the same as your max overclock settings before the pill tho. It will be slightly less so just play around with the values.
actually i havent noticed any difference in stability no matter what order i start them in.
just need sane clocks once in on the pill. once you find that and set it via ab or whatever, it just works whatever order the rig fires them up in.