The sky camera entity (there can only be once, placed in the skybox itself) represents the center of the map. You can say that it is the view of the skybox as seen from the co-ordantes of < 0, 0, 0>.
One way of making a sky box that is coreccly aligned with your map is to place a skybox camera at the < 0, 0, 0> point of your map, select everything and copy it to an enpty space on your map, scale it down to 0.0625 (1/16) (use CTRL-M, and set the scale parameters), makeing sure you have set it to scale textures with geometry, and then delete the original skybox camera that is atill at < 0, 0, 0>
That will leave you with a reference copy of the map that you can build the skybox around, deleting all entites and brushwork that are not needed in the skybx.
Hope that helps.
(also, makesure you are using the right skybox texture, otherwise you will only be seeing the 2d skybox background, and not your 3d built skybox)