A skybox is basically just a textured model that's rendered behind everything else and always centered on the camera, so all you have to do is change the maps on the skybox's POF file. If you want to know how to make the maps, that depends on which program you plan to use - if it's a 3D modeler/renderer, you just set up a scene, place six cameras, all centered on the exact same spot and rotated 90 degrees from each other (one in each direction, of course), set their field of view to 90 degrees and render each of them to a square resolution (say, 512x512).
As for the subspace, yeah, you can mod that. The original subspace effect uses two POF files. I just don't remember their names. Just change them (point to new maps, make a new POF, etc.).