True, that is probably the most thorough way to go about it. I was working with the audio by itself, and then recombining with the video afterwards, so it was ideal in that case, but all options need to be covered for greatest flexibility.

It can be somewhat frustrating that there aren't always Mac options for what's available in Windows. For that reason, I got a program called Crossover, which is a limited implementation of WINE for OS X, so that I could install some applications that were known to work that way. I use Aften for AC3 encoding, and AviSynth to frameserve video for mpeg2 encoding with HCEnc (indexed by DGIndex). These programs work very well, but there are others that don't run at all, so of course it's not a complete solution.