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Layers are used to make combos appear to be on top of each other.
The layers are as follows:
0: The Default Layer. Below Everything.
1: Below Everything but layer 0
(Sprite layer for Freeform Combos. Between 1 and 2.)
2: Below Everything but layers 0 and 1.
(Sprite layer for Link, ground enemies, and items, as well as pushable blocks. Above layers 1 and 2.)
3: Above Link and ground enemies, but below flying enemies.
4: Above Link, ground enemies, and layer 3, but also below flying enemies.
(Sprite layer for flying enemies. Above layers 3 and 4.)
5: Above everything but layer 6
6: The top layer.
To use layers in your quest, go to Screen->Layers or press F12. You can set the coordinates of the screens to use for each layer. The simplest way to use layers is make a new map for each layer of each map that you want to use layers with. Simply set your Map Count high enough to include each layer that you want to use, and then open your Layers dialogue box in any screen. Press the Auto button under the layer you want to set, and then enter the number of a blank map to use it as a layer. From then on, the layer selection boxes will be selectable for the layers you created.
In the layers dialogue box (but not the layer selector in the main window), you can manually set layers for individual screens, and you can also make certain layers translucent for that screen.