Looks good. Great job. The only way to have more than 3 layers of graphics is to have events on top of everything. I've used that method numerous times. Or alternatively you can lay 2 tiles on top of each other in Photoshop (or other app) and have special tiles available in the tileset just for those special occasions. (hope this makes sense, hard to describe what I mean)
Pushing boxes can be used to evade some enemies in some areas, so it can be useful.