War machines have two profiles, one for the war machine itself, and one for the crew.
You always use the Movement, Weapon Skill, Ballistic Skill, Strength, Wounds, Initiative, Attacks and Leadership of the crew. The Toughness of the war machine is used against ranged attacks and the majority Toughness of the crew is used against close combat attacks. The crew's armour save (if any) is used against both ranged and close combat attacks. Once all the crew are slain, the war machine is removed as a casualty.