You can select abilities while paused. If you are fighting with your fists, click on the ability, then click on your target. If you are already in the middle of the round, then it might take a few seconds for you to use it. You should see the number of uses go down after your next attack.
IIRC stunning fist is essentially a charm placed on the fist, which disappears after one hit. You cast it, then go back to attacking (you don't need to do anything else, just cast it, then click on an enemy once the animation is done/the information bar displays something about 'stunning fist'.