For the love of God don't mix audio in After Effects. Audio is only there to be used as a reference, use premiere.
I agree with the previous comment. Never ever even try to get compressed sound directly out of AE. For that, pretty much any other tool beats it, including QT Pro and some free tools. At best, export an uncompressed file, then do the final convert elsewhere.
Right, I know better than to compress straight out of AE. I just left that out.
What is the compression that works best using QT pro.