@sgali, I addressed this with a combination of Slicer settings and Klipper Macros.
You can reference a configuration document I wrote here: X-In/1-Out Non-Mixing Extruder Config
I have a second document specifically on SuperSlicer, which can be adapted for Prusa Slicer, on how to further automate tool changing: X-In/1-Out Non-Mixing Extruder - Automate SuperSlicer Filament Swaps