Hi Steven,
well, in Slic3r you can choose which part of the model should be printed with which extruder.
Example:
Perimeter extruder: 1
Infill extruder: 2
Support material extruder: 1
The number specifies which extruder (1 or 2) should be used for that task. You can read more here: http://manual.slic3r.org/expert-mode/multiple-extruders
As for the simpfy3d you should read this: http://www.simplify3d.com/support/tutor … extruders/
But I think that if you want a specific part of the model to be a specific color (lets say you only want your bottom left corner to be red ), than you'd have to change the G-code, rather than just shift some setting around.
You could try Slic3r's feature to combine multiple STL files into a multi-material AMF file but I cannot atm, being on the davinci 1.0. You basically split the original design into the separate parts within the 3d modeling program, and export each part as STL. You can read more in the above slic3r link.
In G-code editor, I can see which extruder is being used to print which layer (I only have 1 extruder, so it always says E0)
So if I wanted a model to be, half blue and half red (from bottom up), than I would just change the E command in G-code from E0 to E1.
Like I've said, I would if I could... but I cant. So I could be wrong.
Davinci 1.0&1.0A with repetier 0.92 firmware & E3D bowden
Slicer - Simplify3d/CraftWare/MatterControl/Repetier Host
Filament - ABS, PLA, FPE, LayWood
3D modelling - Autodesk 3DS Max, Blender,