I've made some modifications to a python post-processor called filaswitch (see on github) to allow use of of Prusa MMU. Checkout the cfgfiles branch:
https://github.com/paukstelis/filaswitch/tree/cfgfiles. There is an S3D profile included (might need some tweaks) that you just have to duplicate and set the main extruder and the infill extruder to the appropriate tool heads for each filament you use.