Anything thats named as a parallax, for example par1-1 will be set above your character. If you want it to be so that your character can't pass through name it ground. Then while in the editor make any areas the character shouldn't walk through as unpassable.
Basically Yami's overlay's are broken up into 4 parts.
Par- A parallax, your characters will pass under it, like tops of trees or wooden beams.
Ground- Anything else really. Could be flowers, carpets, etc or you could create a stack of boxes in which case you need to mark the areas as unpassable.
Light- Any light effects
Shadow- Any shadow effects.