What you can do is group all your Color layers, I mean the diffuse Layer and give it a name to the group like "Color"...then if you want create another empty group and copy all the relavant layers that could be used for Incandescence for example and put it in there so is all well organized. Then add new layers or modify the copied ones to finish your incandescense map..which could be in color or black and white depending on what it is....do the same with another group for Tansparency or Specular or wahtever else is needed to achieve a convincing render.
Then Export each one as a separeate flattened file for Transparency, Color, Spec etc... and apply to the apropriate channels.
Diffuse=Color
Transparency might involve and alpha channel as a Targa or PNG.
Specular will be black and white and Bump too, maybe as a tiff 16 in that case if the object will be near camera.
This way is organized and you can return to it if needed and adjust anything that is not looking good.
Some other artists might have a slight different appoach but that's a start.
Digital tutors and Gnomon have great tuts....hope thats what you meant.
Best of luck.
