In regards to the hitbox, if you followed the 'how to make a platform game' tutorial (which I HIGHLY recommend), you would see that it is vitally important to make your player an invisible box, then attach a player image to that box. That way, animations will not change the hitbox.
I'm not sure what you mean by 'aligning' these animations... could you be a bit more specific?
A way to set a z-axis? Well, there is no way to do this automatically, however it is definitely possible.