I tried to explain it to you in the AoK Graphics thread but let's repeat:
A polygon has 4 vertices, each vertex has position (world coordinates, when making 2D engine all your Z = 0) and texture coordinates. If you elevate some of the polygon's vertices you only move its world Y coordinate and keep the texture coordinates and let hw rasterizer do all the dirty work for you. Your engine looks like it's using 3 dimensions so when elevating a tile, just raise the tile's vertex's Z coordinate and keep the texture coordinates. It should do the work.
I understand the method behind modifying the vertex coords to create the elevation effect (the screenshot I showed you uses it). The problem I have is that the AoK tiles are already in isometric perspective, if they are simply used as a texture for the terrain it looks pretty crazy. Do you use quads orientated to face the screen or 3D terrain with the tiles applied onto them in some way?
Sorry if I'm missing something, graphics programming is not my forté, and thanks for the info so far.
Here is an example of what I'm talking about...
Aha! I get what you were saying now. I was assuming that the orange border in your diagram was the quad for some reason. It's much clearer now