Well I've never used Fractal Terrains, or Photoshop for that matter, so I can't speak to the first part of your question. However I have worked quite a bit with GIMP and Wilbur, and in my experience (Fractal Terrains aside), it is no easy task getting random cloud patterns to match up with your outline. However, it is possible to generate random cloud patterns in GIMP (or Photoshop) for both your land, and separately for mountains, use the Free Select tool (or whatever it's Photoshop counterpart is called) to select portions of clouds from your Mountains clouds layer, and then copy and paste them onto another layer above the layer of your Land clouds layer. From there you just fade the edges of the Mountain clouds and then use your Airbrush tool (set at low opacity) to sculpt the surrounding terrain to fit these mountains. I recently wrote a tutorial on this process. Of course, if you are planning to generate the clouds in Fractal Terrains, then I'm afraid I cannot help you there.