Make sure you are setting the Compile for setting to “MultiMarkdown”, so that the Processing pane can work. If you set it to “MMD → HTML” then it will use the hard-coded command line and ignore any settings in the Processing pane.
You may also find this thread useful, where this same workflow is discussed in context of Windows settings.
I’ve also updated the clean-compile.zip file in the previous thread to include both a Mac and Windows example. The only real difference is the path to the executable. I also disabled access to this Format from all compile types other than plain MultiMarkdown, since that seemed to be causing confusion.