Colour Mixing

I'm trying to print an object with different mixtures of colours. Currently the only method that seems to be working is to split the stl file in MeshMixer, and then set each part to a specific mixture in Repetier. This method seems to work for simple blocks, but any objects with a more complicated shape prove to be difficult to fit together.

Has anyone come across a simpler method of segmenting a complex shape with varying mixed colour ratios?

Thanks
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