lol, the program is PhotoShop, and it's more about the technique than anything. I started a tutorial a while back, but actually explaining how I do it takes about a thousand times longer than actually doing it.
I put the tutorial on hold because AH2 may change some of the steps... I can't say for sure until it's out.
In a nutshell... I take those 3 files and build a new terrain with it in the TE (you don't need any field info for this method). From there I Export the elevation data, use the Make Map function to indicate the shorelines, and use those 2 images to construct all of the layers that make up a topographic map.
It's no secret, it's just complicated to explain... much easier to actually do.
I can send you my PhotoShop file when I'm done, so you can see how it goes together.