I've got a RT character who has recently acquired an Amulet of Warding (on page 137 of the Inquisitor's Handbook). Does the effects of this device stack with the AP of that character's armor?

yepper is dose. However, it's not so much that it stacks with armour but more like it reduces the damage of the incoming attack (without any benefit of the attacks Pen) before the attack even hits the armour to begin with.