There is support for tile layers. Open a .nw file in notepad and look at one of the BOARD lines.
PHP Code:
BOARD 0 57 64 0 J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4J4I2GRC4D3Dnf/f/f/f/f/f/f/f/f/f/
The second 0 is the layer that this line of tiles will go on. Sadly, the offline editor doesn't support tile layers so you will have to use an online one to add tiles to layers above 0 or simply copy code from one set of tiles in a .nw and change all the layers to another one.
Anyways, for those who already know about tilelayers (This thread isn't about teaching tilelayers to people so let's stay on topic please): Has anyone else experianced this ploblem? Care to give insight to solutions or similar problems?