I am working on a Libgdx game which loads Tiled maps. The current map I am working on makes use of two tilesets, one for shadow/light and another for terrain and buildings. The general process I do, that has been working fine, is that I receive the sprite sheet from the artist, design the maps, then take the spritesheet file and split it using ImageMagick. From there I take the split images and create an optimized png and atlas file with TexturePacker.
However, this is the first map I have made that makes use of multiple tilesets. The issue I am having is when loading the map with AtlasTmxMapLoader it relies on a single atlas file property in the map. I tried to merge my 2 images into a single atlas/texture (keeping the same names/indexes) but it only seems to render by first tileset tiles.
Perhaps I am missing something simple. What is the correct way to handle multiple tilesets (how exactly should my atlas file be setup)?