Hey Juddman,
First off thank you for the tool. I ended up using it as a starting point for a small RPG im working on and it gave me the motivation to actually start something and stick with it

I have a change to the application that I need make for my own purposes but I didn't know if you wanted to be involved in it as an additional feature to your application? I have a tile set that I'm using that has some tiles that are larger that the tile width and height( but still even multiples such as 64x64, 96x96), a tree for an example. Currently if I place that tree on layer two it will anchor to whatever tile i select and render accordingly. The problem come when you want the char to walk behind it. Obviously if hes below the the trunk of the tree you want him to rend on top of the tree but if he's above the the truck he needs to be behind the foliage. Obviously the truck should be the only tile that performs any collision detection as well. This problem worsen if your truck is bigger than that tile you selected then make collision detection even worse.
I don't have the code design yet but here's my solution (That may have some kinks that still need to be worked out). I was thinking of making some type of advanced tile pallet for your editor. Basically I could define a reusable "stamp" that would place the trunk on a defined layer in the selected tile have a defined type that tells the game it's not a traversable terrain (for collision detection) and then place the foliage on level 2 in their own tiles with their own defined types. So as a result when using these tiles from the "advanced Pallet" the tool would place multiple tiles that all have their own attributes.
The tree is the simple example. I have some elaborate cliffs that may be 3x3 in tiles and only one tile is a traversable terrain type but i would go nuts if i have to break out the cliff into 9 tiles!

Buildings are another good example too
I would love to hear from you and your thoughts. My email is
Jeremy.R.Corson@gamil.com.