I know you can use 16-bit grayscale heightfield PNGs to define height. As far as layers go, I haven’t had an application for this. If I wanted to paint layers in an external program, it might be to a texture that would then be imported into the engine and used as a material mask. I think I saw there was an option to import layers, but I’m not entirely sure how that all works.
Manually painting landscape is actually really fun, though! You can even use textures as alpha masks to give you nice variance when you paint!