Cura and Slic3r are able to process multicolored objects. For them it's just to have two stl's, representing the right and left extruder. When you make those dual colored objects yourself in your modeler, remember that they have to be exported with respect to the shared coordinate system. So in FE Sketchup, select the first mesh and export and select the second and export.
In Slic3r you have an option to merge those stl's to a new (AMF) file and slice it. About the same in Cura: select the two stl's on the plate, right click and choose the merge for dual extrusion option.
I have a test dual stl attached on this post.
Cura two single stl's
Cura, two stl's merged
Repetier: result Gcode including support
Bart