I would put 6-4-3 on the hitter, 6-4 on the runner, and then put a line up the side of the inning, joining the two in a little bracket. If it is the 9 hitter and the 1 hitter (e.g. they are a long way apart) then I draw a short line out to the side and put a circle with a one in it for the runner and a 2 in it for the hitter (or a 2 and a 3 if it is the 2nd and 3rd out).
As for the runner, on all put outs on base runners, I put a line halfway to the base they were running to and then a small x at the end of the line. So in this case, the runner on first would get a line halfway to second and then an x.