D A I K A T A N A   E D I T I N G

If you have not been successful in getting a basic map to compile and run in-game yet, then DO NOT CONTINUE. Go back to the Making Your First Map page and get that done right first. No point in reading about skies if you can't see your results.

For the most part your skies are just something you need to setup in the worldspawn class, but you do have to indicate which brushes are going to appear to be your skies.

Point your cursor at whatever brush you want to appear as a sky, and SHIFT-LEFT MOUSE in the 3D window to select that brush. Hit S, and the Surface Inspector will come up. Check the SKY checkbox, hit APPLY, and then close.

Now, in your 2D window hit N for the entity inspector to come up. In the upper right hand corner, use the scrollbar to go down to Worldspawn. Left-click this once, and then you can input the following options into the Key/Value areas to tinker with your skies.

sky             - skybox name
cloudname       - name of cloud texture to use, no suffix
cloud1speed     - scrolling speed for layer 1 (default 1)
cloud2speed     - scrolling speed for layer 2 (default 4)

So, say you were using the E2M1 texture set and wanted to setup your skies in Worldspawn. You COULD try the following:
sky e2m1
cloudname e2m1tile
cloud1speed .5
cloud2speed .6

The above are the basic options for skies, but the worldspawn class allows for a lot more functionality. Test these out and see how you like the results.

cloudxdir       - cloud x scroll value (-1 to 1, default 1.0)
cloudydir       - cloud y scroll value (-1 to 1, default 0.8)
cloud1tile      - number of repeats of layer 1 cloud texture (default 8)
cloud2tile      - number of repeats of layer 2 cloud texture (default 2)
cloud2alpha     - translucency of layer 2 (default 0.7, 0 means no layer 2)
lightningfreq   - min seconds between lightning flashes 
                 (default 0.25, 0 means no lightning)