This gets complicated. You need to actually mix the audio, which to my knowledge, isn't possible with FFMPEG. The other problem you're going to have is loss of quality if you take an MP3, convert it to WAV so you can work with it, and re-encode it back to MP3.
I think you can use Sox for this: http://sox.sourceforge.net/
Use FFMPEG first to decode the audio to WAV, adjusting sample rate and bit depth as necessary.
Then, call out to