So after killing the 3 thalmor guys in Markarth's understone keep. The guards understandably go ballistic and try and kill me. I sheathe my weapon and they dont except so i unsheath resheath a few more times nothing so then i leave understone to markarth and try a few times there nothing. So my question is how do you get guards to accept your yeild and let you pay your bounty?

My guess is there may be a threshold on crime severity where the guards stop trying to apprehend and upgrade your warrant to "kill on sight." I believe a message on one of the load screens states that guards will attack on sight if your bounty is high enough.

I think you meant "accept yield".