Ok, for beginer mappers, I haved a Mapper experience on a game called sickmafia, also a mmorpg of pokemon, you could enter there with a link I will put at the end of the topic, layer 1, is for ground things, grass, tall grass and paths between others... the layer 2, for things that the player CANNOT PASS THROUGH, buildings or trees, layer 3,is for things that the player can walk down of it, the layer 3 should always be used in the top part of buildings.
All this I wrote, sickbailey tell it to me, he is a great person and I hope he helps us.
Here is the link to his forum:
sickmafia.zxq.net
Enter there and regist, I put the link because he is my friend and I want his community be full also.