I have often done maps in Photoshop painting textures with a bevel/contour, and have like the fact that it would create what appears to be a textured height map. Then I could paint terrain onto the map that follows the background texture of the map.

I would like to know if there is any way that I can take an output from FT3 and do something similar.

Here is a sample of what I am talking about...
Click image for larger version. 

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Notice that you can still see the hills and valleys through the woodland colors.

FT3 does a much better job at generating an altitude map, but I like the painting tools in Photoshop.