As for the how to:
The "Takes place inside subspace"-flag makes the engine use two models for the skybox (SubSpace_Big.pof and SubSpace_Small.pof) which are basically cigar-shaped and rotate - one clockwise, one counterclockwise.
Their maps for "skyboxes" are Noise01.dds and Noise01b.dds.
Both the models and the maps can be found in mv_effects.vp or sparky_fs2.vp (the maps in retail VP are 256x256 as opposed to the 1024x1024 in the MVPs).
Note that any change to the maps carries globally (it can't be set mission to mission because of unique two skyboxes thing).
Note also, as the maps use black as transparent colour.