When shooting at a war machine (including spells and template attacks), resolve the attack as normal, using the Toughness value of the war machine. The crew's armour save is still used to attempt to prevent any wounds inflicted.
In case the crew of the war machine is made up of models with different profiles, such as a character or other unique crew model; allocate the hits between the crew as you would for shooting at characters in a unit (see the Characters chapter).