Hi, I'm not sure the TMX would help you as a this point it's a mess of me pasting the new tiles over the top of every time I update the tile set! I also tend to do everything by hand instead of using the auto-tiling and probability features in Tiled, although the tileset is designed to let you use these features. In future updates I'll look at including some templates to make getting started easier. In the meantime I can give you a break down of how I go about building up maps though.
I pick a base biome depending on what the most common terrain type will be for the map - usually grass or wasteland. Other biomes are added on top in separate layers, they're designed so they can overlap each other in different ways. If I'm using the multilayer tiles then water is usually the top biome layer because the shore tiles can overlap all the other terrain types. Then I add layers as needed for smaller details like trees, roads and rivers, structures and mountains.
For the single layer version of the tiles, you can build this up on a single layer or use multiple layers for easier editing and flatten at the end.
If you want to use auto-tiling there's a reference image showing how the tiles map to Tiled's corner based auto-tiling algorithm. There's many different ways of doing this depending on what works best for you. For the multilayer tiles I usually make a terrain set where the edge of the biomes transition against a "null" or empty tile and fill the biome layer with this null tile so I can draw in the shape of the biome on top of this. Then for "sub-biomes" (e.g the lighter grass, trees on the single tile layers, cobble stone or paving) I have these transition against the base terrain type so I can draw these in on the same layer. Trees can autotile, but mountains are placed by hand and have a repeating pattern (this is another thing I'm looking at making easier to use in future updates).
The tile set isn't designed to allow for transitions between more than two terrain types in a terrain set as it would be unworkably large.
I hope this helps you get up and running!
- Matt
