I've created this dedicated thread for any discussion or questions regarding BD3D2MK3D.
If you want to convert your 3D MKV file ripped with MakeMKV into an SBS file, this is a good program to use.
The author of this program is r0lZ.
http://forum.doom9.org/showthread.php?t=170828
"BD3D2MK3D is a GUI to convert movies from 3D BDs to 3D MKV video files in Full or Half Side by Side, Top & Bottom or Frame sequential format, encoded in h264 with x264, or in h265 with x265, or with any command-line encoder. Since v0.87, BD3D2MK3D can also accept lossless 3D AVC+MVC files created with MakeMKV as input."