I've been using S3D with my CTC and wanted to expand my skills and ordered a Prusa i3 MK2 equipped with the multicolored printing. I wanted to know if S3D will allow me to configure multi-colored prints within the application?
There have been a lot of color mixing extruders over the last few years and I've used S3D with several of those just fine. I would think the process would be the same for the mk2 (it uses the same technique as a lot of the other extruders that already existed).
The firmware usually works by assigning a virtual "tool" to each color. So then you just switch to that tool to print in a specific color. You can usually choose what colors you want to setup for a print, but then it's no different than any other multi-extruder printer.