The simplest way to add audio to video file is by AddAudio method. It works for most cases. By default it takes first video stream from input video file and first audio stream from input audio file and all subtitles from video file. It can work unpredictable when you will try to change format/extension of input file.

string output = Path.ChangeExtension(Path.GetTempFileName(), ".mp4");
var conversion = await FFmpeg.Conversions.FromSnippet.AddAudio(Resources.Mp4, Resources.Mp3, output);
IConversionResult result = await conversion
    .Start();