First off, it only works with Optifine or MCPatcher installed, so install one of those (Optifine is best). In the folder for the resourcepack you're making, navigate to minecraft and add the folder 'mcpatcher'. Open that folder and make a folder named 'sky'. In that folder, create another named 'wold0' and finally, in that one place your sky image file. To make the sky image file, create a png image that keeps the dimmensions (can make it larger or smaller to change the res) of 1536x1024. Name the image file 'sky1'. Make the image black and then draw the clouds (I'm assuming that's what you want to add). The sky image will be split into 6 pieces by Minecraft and mapped to the inside of a square which surrounds the Minecraft world.
Also inside the 'sky0' folder, create a .txt file and name it 'sky1'. In it past the following:

startFadeIn=5\:00
blend=add
rotate=false
endFadeOut=18\:00
endFadeIn=7\:00
source=./sky1.png

If this poorly written tutorial doesn't work, you can always download a resource pack that changes the sky and look in it. Two I know of that do this are Athery's Ascended and BackyardCraft. Athery's Ascended might be the most helpful for learning how to do it (It's what I used).