A video file and an audio file (that contains 2 channels) - Map the video to stream 0 of the resulting file and the audio file to the next stream/s.
ffmpeg -i video -i audio -map 0:v -map 1:a output
NOTE: Channels are conjoint tracks within a single stream, so a stereo audio has one stream which contains two channels.
ffmpeg -i video -i audio -map 0:v -map 1:a:0 -map 1:a:1 output