Quote:
<Highest>
Layer 6
Layer 5
Flying enemies
Layer 4
Layer 3
All other enemies and Link
Layer 2
Layer 1
Combos on the main screen (this is often called "layer 0")
<Lowest>
In other words, layers 1 and 2 are under all enemies and Link, but will appear over top your main screen's combos. Layers 3-6 will cover up Link and all enemies. Layers 5 and 6 will cover up not only those, but also flying enemies. In this case, you would want the tree layer to be on layer 3, 4, 5, or 6. If you specifically don't want flying enemies to fly under the tree layers for aesthetic reasons, put these tiles on layer 5 or 6. Simple as that.