I contacted S3D support and asked this question: Does, or will, Simplify3D perform/slice and write G-code for multicolor prints for Prusa's MMU2S?
This is their reply: "Thank you for your question. I am happy to help. We are currently working on better support for the Prusa MMU 2.0. Simplify3D already supports up to 6 extruders, so it can be used for the MMU with a custom profile. The tool change retraction is somewhat poorly documented for the MMU2, so please watch this closely and let us know if there is any unexpected behavior. Please try the attached profile. Follow these steps to import and use the profile:
Download the attached file.
Open Simplify3D, go to File > Import FFF Profile, and navigate to the saved profile. This will import the settings into the software.
To start using these new settings, click Edit Process Settings, and the choose the new entry at the very bottom of the Select Profile drop down list.
[EDIT - Contact support as recommended above if you need the profile]