After you liberate an outpost, certain "jobs" will be posted on a bulletin board. These jobs will be given icons on your map if you apparently have trouble finding them.
The WANTED Dead quests require you to kill a commander with your knife. There will always be "regular" soldiers around the commander. Deal with these men as you wish. Either gun them down or knife them as well by using rocks to lure them away from the main group.
As soon as you kill the commander with your knife, the quest completes and you are awarded the trophy.