Usually, what you’re describing is exactly what you want: by leaving the IK target independent of the pelvic bone, you can easily have the bird bob up and down. If you want to move the entire bird as a whole, you’d either move the armature as an object (presuming the bird object is parented to the armature), or you’d create a new root bone, to which both pelvis and IK targets were parented.
But it’s not like there’s any right way to animate, just whatever is most convenient for what you want to do. If you want the IK targets to move with the pelvis, parent those bones to the pelvis.
Hi, as bandages all ready said the pelvic usually don’t control the leges, you should have a root bone in your armature to enable you to move all the controls of the character together.