So I have been reading up on Vertex color, because I need to use it for the blend layer inside cryengine 3. So from what I read about the blend layer I will need a vertex alpha channel and a blend map. And what I can gather from the crydev forums that the blend map is just an alpha map. So is the vertex alpha channel something that you save into the mesh it self through vertex color ?
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If you want to save your vertex colors to texture then open the options for the Paint Vertex Color Tool, look under Attribute Maps and Export. Should be straight forward from there.
It's just a matter of painting the vertex color alpha information and exporting the mesh. The generic "blend map" is not nessecarily created in Maya, more than often I'm guessing you create this in Photoshop using a heightmap as a base.
There shouldn't really be a need for you to "bake" or transfer the vertex colors to texture from what I can tell.
I've played around with doing similar things with my own shaders, although instead of using vertex colors for defining placement of material A & B, I've used a texture.
all the blendmap does is tell the engine what areas to blender the vertex paint into first.
Thanks for following up with your solution though on the color-set editor - i know a few people who ran into similar problems with it!
Picture: http://imgur.com/shPkefc