Once you add the subtitle, you can start converting your video. Click the "+" button and you will be prompted for the subtitle file.
The click "Filters" and select the option "Subtitles" option and then one of the available options, depending on the subtitle format. Then click the button below the Video options, next to the video preview and select "MPEG-4 AVC (x264)", which is the encoding method you want. It's not exactly a second track, because the video was separated from the audio stream when you extracted them form the mkv, but this is the way it works.
You need to open the video stream in avidemux, then add the audio through "Audio > Second Track". Then you have to put them back together, but this time physically embedding the subtitles over the video and econding the output (video+audio+subtitle) to the format you want, which is a mp4 container encoded with h.264 codec. Once you have extracted them, you will have at least 3 separated files, one will be the audio, another one the video and another one the subtitles. So, if they are not physically tied together, you can extract them right? Yes, you can extract the subtitles, the videos and the audio streams from the mkv containers, using the extraction command of mkvtoolnix application (consult mkvtoolnix instructions). The same applies for videos and audio, which basically means you can add any number of subtitle, video and audio streams to a mkv container, without actually physically merging them. It has separated subtitle files, called streams, inside the mkv container.
The matroska format does not embed the subtitle in the video itself. You have a couple of matroska (mkv) files with subtitles included. What specifically do I need to do? You are really confusing me. So I'm trying to convert to mp4 for my mp3 player, and i need to render the subtitles from an mkv video to this new video.
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