1: You can define where clouds show up in various ways. For your specific purposes I would use a through-camera-projected Image Map Shader as a Blend Shader input of your Cloud Density Shader input. Render the scene once at low detail, then open the resulting image in an image editor and create a gradient or hand-drawn mask that has white where you want clouds to show up and black where you don't want them to show up. Use intermediate shades of gray to smooth the transition. Save as BMP then load this image in your Image Map Shader.
2: I don't think you can turn off the shadows just on the terrain at this point. The best you could do is turn off "enable secondary" in the cloud shader, render just the terrain with a crop render, then composite with a normal render of the top (with enable secondary turned on).
3: You can't control clouds to this degree yet, although you can use image masks, either through-camera or Plan Y projected. Through Camera will allow you to directly define the cloud shapes *as they will be seen by the camera*, although getting realistic edges and shapes can be difficult. Plan Y lets you define the cloud shapes using a mask projected from above. Use the above described technique to mask cloud shapes in this way.
4: The acceleration cache is a rendering optimization that speeds up cloud rendering, but can sometimes cause visual artifacts. That's why there are multiple settings available. If you get strange lines in your clouds in a scene, try turning down the acceleration cache.
- Oshyan