Getting StartedΒΆ
Using MKVToolNix do any desired operations on the first media file in the source directory. When done copy the resulting command line to the clipboard:
Multiplexer->Show command line

Copy to clipboard
Open mkvbatchmultiplex and paste command using the <Paste clipboard> button:

Copy from clipboard
Now there are two options if there is only one source directory to work with press <Process> button. To work with more than one source directory press <Add Job>. <Process> intended to start working immediately on the job at a time. Even though the jobs generally are very time consuming there is a very simple job queue system working <Add Job> adds to the queue when done press <Process Jobs>