Consider support of the mosaic multi color platform.
I believe it can be integrated into the slicer with an option.
Will work without direct integration but it would sure be simpler.
They will integrate with slicr and want to work with other software like Simplify3d.
Please contact them if you feel this would benefit the simplify3d platform.
Thanks
They are at http://www.mosaicmanufacturing.com/