A war machine unit comprises the machine itself, plus its crew. As the crew aren't really a combat unit, per se, we ignore them for most gaming purposes, treating the war machine itself as the extent of the unit. When the war machine suffers a wound, remove a crew model. Once all the crew have been removed, the war machine itself is removed from play. Similarly, if the war machine is removed as a casualty, all remaining crew are also removed. The crew are used only to indicate the remaining number of Wounds and the number of attacks the war machine can make in close combat, so players should simply arrange their crew in a pleasingly aesthetic fashion within 1" of the war machine.
The crew cannot be charged, attacked or otherwise affected separately from their war machine – if they are found to be blocking movement or line of sight, the controlling player simply alters their position, just as you would for any other battlefield marker or counter.