You should use the multichannel devices, hw:x,2 for capture and hw:x,3
for playback. This allows you to record mic and line in separately.
The inputs should appear on 4 different JACK ports, out of the 16. You
will have to use trial and error (meterbridge helps a lot) to determine
which inputs correspond to which JACK ports.
This configuration bypasses the mixer completely.
See Documentation/emu10k1-jack.txt for more info. ALSA 1.0.9 or later