Your joints will never be 0 0 0 unless you want the joint sitting directly on top of its parent. Like I said, all joints will have some sort of offset from their parents. Usually, it is along the x-axis.

If you're getting weird twisting when manipulating IK handles, it could be because the local rotation axes of the joints in the IK chain are not oriented correctly. Quick solution is to run Skeleton > Orient Joints on the entire joint hierarchy before creating the IK handle.