Some lightmappers use layer 0 for the shadow maps, some use layer 1, in the end it doesn't realy matter. You may use them with the multiplying blend mode, or multiply blend 2 thingie. So the darker a lightmap texel is, the "less fullbright" will the final mix be.
Not sure about Colormaps, never use them. You may also make use of Vertex Colors, btw.
I don't understand your question about terrains. You may use a texture or a brush. A brush may also contain textures. It's kind of a containier for material properties.
Blitz Terrains may not be very useful since you can hardly use multiple textures with them, and they also "pop in" due to LOD, I'd say they are good for water, but that's it.
I'd rather use a meshbased Terrain tool that is using vertex alpha to blend various textures. Remember Rifrafs relase of the Free Landscape Editor - that unfortunately has vanished from the servers.
Considering the fact that this was an open source project I really think about to add some userfriendlyness to the wip version that I currently use and release it the sooner or later.
There are more apps of this kind, like ALE oder CLE:
http://www.blitzbasic.com/toolbox/toolbox.php?cat=7