While audio transcoding isn’t as CPU-intensive as video transcoding, it’s still a good idea to maximize compatibility where you can. When it comes to configuring your audio streams, we recommend using the AAC (avcodec) for any stereo tracks, and AC3 for any surround-sound tracks. Between them, AAC and AC3 should offer at least one track that direct-plays on any playback device. If there’s only a single stereo track, simply create a single AAC (avcodec) track; if there’s only a single surround-sound track, however, create two audio streams from it—one downmixed to stereo (AAC), and the other preserving the 5.1 surround sound mix (AC3).
The other consideration is bitrate, which ultimately determines the quality of the audio stream: again, your personal preference will determine this, but as always, the higher the bitrate, the…