the tokens overlap when they are in the same square. because there is no 3d environment stuff flying/burrowing/swarm/tiny creature tokens all overlap. as a fix i think a few extra layers for the game would be useful. these layers would need to be viewable by players and gms assuming that character can see that part of the map. i was thinking these layers would be tied to either the token or map layers.this would make it easier to deal with creatures like flying/burrowing creatures that are occupying the same square as another creature.