Carbon already answered your questions but I'll give it a go as well. I'm not a graphic artist so I don't know the the intricacies and specific technical details so much but I can give you a run through of how I go about things in Photoshop.
The cl and da textures are both single layers in Photoshop (PS from here on out). They must be a single layer in order to save as a dds using the NVidia plugins. They are, however, RGB format so they do contain R, G and B channels when you switch to the channel view in PS. To add the Alpha you add in the channel view/setup, not in the layers for the file. It does not effect the actual complete visual sum of the texture and seems to be used purely for data in SoaSE. The Alpha channel is not added by default in PS and you have to manually create it on a new texture (right click in channel view and add a new channel, Alpha is the default result). As I mentioned previously, leaving it completely black/blank does not produce the desired effect. I have found it necessary to adjust at least one pixel in it for it to work properly, although that pixel doesn't even have to be inside the UVMap section of the texture. This may be a PS/Nvidia plugin thing and may or may not be the case in Paint Shop Pro or GIMP.
When you save the texture as a .dds using the NVidia plugins, the alpha channel is treated as transparency. I'm not sure what the proper format is, but I use DTX 5 format with 8 bpp transparency when I save to .dds for Sins.
For the color map (cl) texture, the RGB channels are used as a standard image. By that I mean they are summed to create the end visual result as they would be in a normal image. The alpha channel is used for team color. It is in grayscale and the white level determines the amount of team color applied to the underlying section of the texture. Black is no effect, white is complete override with team color and varying levels of gray can be used linearly as desired.
For the data map (da) texture, the image is not treated as a sum of the RGB channels. Instead each channel is treated discretely for a desired effect. R is specular, meaning metal "shiny-ness". G is light emitting and any data on this channel will result in the relevant sections of the ship giving off light in game. B is reflectiveness and gives the relevant sections of the texture mirror like qualities. Alpha is used for bloom and should therefore typically be used in conjuction with the G layer (since you'd normally only want bloom on something that gives off light). Once again, they are linear values and you can use the desired amount between 0 and 255. Don't worry about what the combined RGB output is since it really doesn't matter. Most often my da textures end up looking purplish with green highlights and not anything like my cl map aside from some general shapes.
I can't speak to much about the normal map (nm) texture. It's bump mapping but I haven't done much playing around with it. The guide I used while learning advised just using the PS filter that Nvidia plugins add to create the nm from the cl texture and so far that's all I've really done. I suspect that this is not really the correct way to handle it in Sins as my understanding is that Sins doesn't use the normal map in the traditional sense. For now though, it seems to be working adequately enough for me.
If Carbon's responses didn't clear up all the questions, hopefully this fills in any of the remaining blanks.
-dolynick
