As pupils are usually black, you will not be able to make them glow unless you change the color of the pupils to a different color in the color map (texture). In other words, if you want the pupils to glow red, you will need to make the pupils red in your color map. Also, the areas you want to glow will need to be white in your glow map and the emissive color, in the nif, will need to be some color other than black. I hope this helps. The same applies to transparency. Any area you wish to have any transparency show up in game must have a color other than "total" black (0,0,0) to work. By the way, I use 8.8.8.8 (uncompressed, alpha layer, and "all" mipmaps) for all my textures.