When I move my root bone, that bone in the head turns orange and moves last with quite a bit of stubbornness. Only happens when auto IK is on so i’m assuming the IK is thinking the head bone is a foot. How would I go about changing that behavior to happen on the feet instead of the head?
We need to see a blend file with the problem in it please.
Auto-IK is not a solution I would use for much of anything. It looks like you already have some constraints on bones, so go ahead and create the IK constraints that you want. Don’t use Auto-IK.
From the Blender Manual:
The auto IK option in the tool shelf enables a temporary ik constraint when posing bones. The chain acts from the tip of the selected bone to root of the uppermost parent bone. Note that this mode lacks options, and only works by applying the resulting transform to the bones in the chain.