I'd recommend looking into ecasound
http://ecasound.seul.org/ecasound/

I dont think its been built/packaged for fremantle (It works for me in a debian chroot though) but if you can get it to record from the appropriate pulse syncs, you can probably have it grab/mix both streams at once, or possibly just use one per stereo channel.

Failing that (it doesnt seem to directly support pulse), im pretty sure it could mix the streams after the fact.