1 - I have No idea, but Nowe seems to know.
2 - As Nowe said, you gotta make a mask in GIMP or Photoshop using the standard RGB colors. Pure Red, Pure Green and Pure Blue only.. Don't use colors like yellow or textures will mix and look ugly. And ofcourse you use the same 513X513 pixels as heightmap, only diff is heightmap is in greyscale, mask isn't.
3 - For that you just go to Sky Maker and you scroll down and change the sky colors and sun colors for diff times of day and at the end SAVE as whatever name you want it. When you in Map Maker on your map, go to World > Sky File and then you type in the name of your custom sky exactly as you saved with capitals and all. Don't forget to make sure the Sky box is ticked.
For custom weather as in rain and snow etc, that is also in Sky Maker but under Weather. You can choose there how fast the snow particles move by, for example, then you save that as well and type in the name of the Weather File under Weather Cycle File in Map Make
But for custom weather like snow etc, I suggest looking at tutorials on how to set when the snow comes on and fades away as I hadn't tried making custom weather yet