I've just pushed an update to the development branch of PCBmodE here. This update includes support for multiple layers, although only top and bottom are tested for now. (Everything is set to define more than two layers, but I haven't constructed a board to test it, so it will be officially supported at a later time.) I also added the 'both' board for testing the two layers. Here's how it looks:
Notice that I have also changed the colour scheme, which is defined like CSS in a JSON file, so it's easy to change and manipulate. Here's how 'pieceof' looks like in this new scheme.
