AutoTune is currently not built into CC3D/Atom firmware, due to small CPU and lack of memory.
Both next and 16.09 (RC's) have AutoTune. AutoTune is not currently built into CC3D firmware, but in the future there may be a special version of CC3D firmware just for AutoTune use. Here is the simplest version of how to use AutoTune for those that don't want details. If you don't read the details (problems to avoid and useful features you didn't know existed) and ask questions that are answered farther down in the details, be prepared for a bit of derision.