Whilst in the midst of working on the different components of my map, I decided to take a break and fiddle. I liked the feel for what cam out of this fiddling, and decided to share what I did.
Fractal Terrains Pro
1. Create your map in FTPro.
2. Export a grayscale (I used 16 levels) image of the land, only, in altitude mode. To do this, I set the water colours to red.
3. Export a grayscale image of the water, only, in altitude mode. You can adjust the grayscale , of course, to suit. I used near white to near black, though I think it may look better as mid gray to dark gray.
4. Export an image of the texture only. This is produced by setting all altitude colours to white, and setting the Intensity to, well, whatever you prefer. I used the default in this example.
5. Export your rivers against, again, a white background.
6. Load all layers in Photoshop, with the Rivers and Texture on the top. Switching those two around differs in the end result slightly.
7. Remove the RED backgrounds of the land and water layers. I use the magic wand, set to 0 for tolerance.
8. Remove the white backgrounds of the river and texture layers.
9. On the river layer, select all the rivers - either by colour or with the magic wand and "contiguous" unchecked.
10. Under Select, modify the selection layer to expand it by a few pixels to taste. This will depend on the resolution of your image greatly.
11. Fill that selection with the river colour of your choice. I hit delete, and then fill it with the painbucket with contiguous unchecked.
12. Under the Hue/Saturation, choose "colourize" and colourize your water layer to a blue tone you like.
13. Under the Hue/Saturation, choose "colourize" and colourize your land to a green tone you like.
14. Set the texture layer to multiply or darken as your prefer.
That was it for this quick map. Perhaps someone can use the effect somewhere. It's nice and easy to do.
You may consider putting a climate layer above the land layer and set it to hue/colour and see how that turns out as well.
Note: This was part of a work in progress, so rivers, etc, don't always work.