Hello The link that Devon posted is the method we're currently using to handle terrain transitions in Story of a Lost Sky.
Here is an image showing it in action http://img.photobucket.com/albums/v189/rune_devros/020-enemyrange.jpg Our tileset demonstrating our map artist Water and Wind created the different transition tiles: http://img.photobucket.com/albums/v189/rune_devros/terraintilesv3.png -Fawkes