I think it's better to convert it to NSF first, then convert to WAV. Why add an extra step? Because FamiTracker's WAV output (real time, and saving to a .wav) is inaccurate. Ever since FamiTracker 3.0 was released, there's been a lot of timing issues where some frames are skipped. Output to NSF, everything plays the way it should.
You also have more accurate NES sound if you output as NSF..you could also have the added advantage of playing back via a REAL NES and get that analog sound that FamiTracker just can't match.
i'd also recommend recording an exported nsf, they just seem to sound nicer than the songs played in famitracker, in a few ways... mixing, noise timbres, notes are a little more staccato as well.
also, unless you're recording stereo from nsflive or notsofatso, you don't need 320kbps (i'd even argue you don't need 320kbps with stereo...) you could probably get away with 128kbps CBR with a mono mp3 and not notice encoding artefacts. then again this IS 2009, so who cares...
I'll note that OGG is better than MP3 in virtually every way. The only thing that MP3 has going for it these days is the fact that there are more programs and devices that accept MP3.
