If you use Workbench or similar 3D dual color printer and Slic3r, you can
1) Make two individual parts, but be better to use a same XYZ coordinate system,
in order to assemble them more easily.
Part-1-RED COLOR

Part-2-GREEN COLOR

2) Use software to assemble them in together:


3) "Save as" this assy file to STL file, then creating two STL files automatically
in a folder that you selected.

4) Open Slic3r and "ADD" those two STL files

5) Use a dual color printer to print this object with two colors.
A same procedure is for 3, 4, 5, 6---colors, if you have a multi-extruder printer.
Attached are two STL files, for you practise only.
Post's attachmentsCP3 ASSY-red-green - CP-3-1-red-1.STL 68.83 kb, 4 downloads since 2016-10-27
CP3 ASSY-red-green - CP-3-2-green-1.STL 45.79 kb, 4 downloads since 2016-10-27
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