One of the best things about the writing process as I experience it is the gradual discovery of what the story is about. Character motives reveal themselves over time. Coming up with a title often gives me further insight.
I don't think I deliberately incorporate layers
in a story. Some part of my brain plants them there. But when I notice a
thin layer, just a suggestion of a theme or symbol, then I consciously
build the layers more thickly. I find places where I can repeat a symbol
naturally. I find ways to echo or point to the theme. I look for places
to make connections.