It can be very useful to work with layers in your maps. You may want to export separate layers (so that your objects can be between them for example) or you can merge them together. But working with layers will result in having to create less different tiles in your tilesheet. If you do merge your layers for export, all unique combinations of tiles will become new tiles in the exported tilesheet.
To add a new layer to your map, select Maps, Layers, Add Layer from the menu. You will see the new layer in the project window. You can easily select a layer to draw on by pressing a number 1 for bottom layer, 2 for next layer, etc. The other layers will become transparent. If you press the same number again, all layers will become visible again.
You can find the other actions for layers in the Maps, Layers menu.
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