Try this perhaps:
rip with makemkv
This will retain all chapter markers from the disc.
Then go and identify which episode is which chapter.
Encode each chapter individually with Handbrake.
Or take the big MKV file coming from makemkv and split it up at the chapter markers with MKVtoolnixGUI.
guide here: [HowTo]: splitting multi-episode files with MKVtoolnix GUI
You can then later send the parts through Handbrake individually.
