the different formats behave differently from what I have experiened... .png has opacity settings so you could make the clouds transparent. .jng has lighting settings that make the sky vibrant and glow. .jpg is ordinary image with nothing applied.
and to answer your question about the numbers? Theres 6 sides to a square but the bottom of the square isn't viewable unless you have a portion of the map missing. So there willl be 5 panels in which you need to skin. left, right, front, back, and top.... thats why they call it a sky box.