More info about transparency in case you don't know:
The transparent color is the color you can see through on transparent layers. You can use it to make multiple layers and allow the foreground layers to let you see through to the background layers. Areas in a foreground layer that use the transparent color will show through to the background layer. But in order for this to occur, you must set the foregound layer to be drawn as a transparent layer by using the checkbox. If a layer is not set to be transparent, then its transparent color will be ignored and it will simply draw the whole view opaquely, covering up whatever is behind it. Generally, the only layer that should not be transparent is the background layer. Furthermore, on a transparent layer, tile number 0 is always assumed to be entirely transparent and is never drawn. This allows GameDev to skip thinking about invisible tiles so it doesn't have to waste time drawing invisible pixels. So keep that in mind if you try to use tile number zero to draw graphics in a foreground layer.
