well, you can put your clip into an FCP timeline,
and Export as AIFFs
i've only used this function once in 13 or so years, so i can't remember if you need to set up a separate audio output for each track or not.
but what i HAVE been doing for years is working with WAV files, without any problem that i'm aware of.
what sort of problems do you have with WAVs?
maybe its as simple as mismatched sequence settings?
nick