I've been working on multi-mono input for Aften over the last 2 days. I'm finally happy with it, but I need to do some more testing before committing it.
I decided to implement it within the pcm reader rather than in libaften. It's a bit slower since it has to interleave the samples, then libaften turns around and deinterleaves them. It makes things simpler though. I have thought of implementing planar pcm decoding and planar aften encoding. This would probably make things faster when using multi-mono input because it would avoid both the interleaving and deinterleaving.