Start with something simple, try to do it with CircleShape2D.
If your body does not have shape or need a new shape, look how changing the shape on the helper wont change the shape on the body (the body keeps reference to the original), you need to change the shape on the body and use a helper only if you need some visuals (you can always
_draw on the body too).
More complex shapes need to be built, CollisionPolygon2D only stores a Vector2Array with points, not the Shape2D.
That is the case of changing shapes, if you modify the shape and body and helper have reference to the same object so you will notice changes on both (not the case of polygons).
ps: All this may change on Godot 3 but I don't know how.