if you media manage as Shane suggests, then the sequence audio outputs are completely irrelevant.
it’s odd that you are being asked to convert the media to non-editable formats like H264 and AAC audio.
i guess they will re-transcode it on the other end?
if your audio is 2 tracks only, then i think that you need to make it stereo and convert it as stereo,
than you have a chance of keeping your two tracks separate.
as i say media manager will not change the audio in your files, just trim them of any excess.
so test your conversion to H264 & AAC audio before you go down this path
you CAN change the audio format in FCP by dragging the clips into a timeline,
and making them stereo. (select all, Option L, CHECK YOUR PANNING!)
you can cull the clips in the timeline, too.
then copy/ paste into a new bin, and do a batch export.
Export as QuickTime movies, same settings, USE IN TO OUTS to trim.
(as you are going to convert all these files to H264 you could export as non-self contained. it’s a lot faster, but risky in the long run)
this will create new files with STEREO audio, which might convert to AAC better for you.
nick