1. You can load the png into a sprite which has pixel perfect collision.
I don't quite understand what you mean by having part of the player sprite underneath, but you can change the drawing order of sprites with "Send to Front" and "Send to back" actions.
For multiple collision boxes you can use another invisible sprite and always set it's position to the player sprite.
2. Change the drawing order of the enemy sprite with the "Place behind another object" action.
Collisions can occur even when objects aren't visible.
3. Here's a behavior that you may find useful for that:
http://www.scirra.com/forum/viewtopic.php?f=2&t=5693