Thou shall not kill?

God says thou shall not kill as one of the Ten Commandments but he actually instructs his chosen people to kill numerous times throughout the Old Testament. Then there is tons of killing, persecution, and even torture performed under the authority of the Catholic Church under the New Testament. Specifically I would like to sight the story of Saul when he is instructed to kill everyone of the Amalekites men, women, and children. Saul failed to do so and he was actually punished for it and would eventually lose his annionted kingship. So in short my question is: Why does God condone or order so much killing when it is against the Commandments?