MKV with all audio and subtitle tracks


New here, so sorry for possible stupid questions. I’m evaluating MCeBuddy with the free version, so I suppose what I’m looking to do might be possible with the premium version, I want to make sure though, before committing.
What I’m looking to do is: I have a bunch of transport stram recorded with NextPVR and I’d like to convert them to Matroska, very basic stuff but…

  1. NextPVR already runs comskip for me and I don’t want to cut the commercials from the output (I’ve never managed to get the output reliable enough) but I’d like to keep the edl in the folder (currently MCEBuddy seems to archive/delete it)
  2. (and this might be the tricky part) I’d like to keep all streams from the ts. That may consist of multiple audio streams and multiple dvb subtitle streams. I don’t really care about re-encoding the audio streams, they’re already pretty small, but compressing the video would obviously be desirable. I’ve played with ffmpeg and while there’s a version that is supposed to handle dvb subs, I can’t get it to work. So my thought pattern goes something like this: Convert the video (only the video) with ffmpeg/handbrake, demux all the other streams from the ts, with e.g. mkvmerge and finally merge the compressed video to the other streams with e.g. mkvmerge. The video conversion surely can be done and mkvmerge can handle the other streams. But can it all be done with MCEBuddy so that sync is maintained?

See this post for DVD SUBS: