You are referring to a similar system as used by the AGS engine? In that engine the developer of the game has to draw a mask over certain sections of the scene that the player can walk behind as well as define the point on the y-axis which determines if the player should be in front of, or behind the masked area.
I believe both methods have their own set of pros & cons, besides it's always a good idea to work in layers when creating artwork, so it should be as simple as only selecting the layer you want, exporting to .png & then overwriting the previous file - maybe reposition a little bit in Visionaire Studio, if needed.