I really like the skull one
The editor does support transparent regions/color keys, but if you import dirtover from Xenimus and try to use it, you'll end up with transparent areas that show the background color (light blue) instead of some other texture. This has because this is a tough issue to solve--I'll explain next.
First of all, I solved the problem last time by hard-coding the dirt-over stuff into the editor (if a fluid bordered dirt, it automatically generated the right kind of dirt overlay). This worked well because it was automatic--no need for you to go around your thousands of tiles of coastline and change every single one. This was a temporary solution at best, and something I hoped to fix with the new editor.
In this editor, there are multiple ways of solving the problem. I could make the dirt-over automatic, as I did before, but that doesn't seem right because it ties the editor to specific content--and the whole point of this editor is to promote flexibility. So another solution would be to introduce a second Map Layer list under Atlas called "Map Overlay". These layers would be applied on top of the layer below and could be used for all sorts of fun things, such as roofs on buildings, in addition to the regular map information definition. The problem with that would be how to update the overlay when you, say, add a new island. There could be a command to generate the overlay, but it would difficult not to make it erase any specific changes you make to the overlay on the coastline. What's more, you'll have to specify some sort of pattern for it to work off of (i.e. tell the program, "hey, if you have any one of these dirt ground types to the north of a water block and, any of these dirt types to the west of it, put this west-north overlay on top of the water).
Hmm...actually that rules thing isn't a bad idea. It could be used to import these textures, which contain blending between grass and bush-like textures, for example:
http://www.lostgarden.com/2006/02/250-f ... tures.html
(P.S. Try using those in the editor, they look really good!)