If you want to install the Bondtech MK3S extruder upgrade and also have the MMU2S, you can use Joe Prints' IR sensor holder design linked below. However, his design is for the Bondtech MK3 kit, so you will need a different top cap for the MK3S upgrade.
I recommend using a PC4-M10 (passthrough) fitting optimal feeding, but I have also included a file for a PC4-M6 fitting. In either case, it is a good idea to manually chamfer the inlet of the "Adapter-printer-mmu2s" to ensure a smooth filament path.
Since Bondtech doesn't provide a modified firmware for the MMU2S, a simple workaround is to simply flash the Bondtech MK3S firmware first, then flash the Prusa MK3S-MMU2S firmware. The critical settings from the Bondtech firmware are not overwritten by the Prusa firmware (at least not for 3.7.2).