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FamiTracker
If I were you, I'd use the WAV import function to output two WAV files instead of one for stereo mixing (if you're actually trying to do something more conventional with audio editing).
I'd first dump one of the square channels & the triangle as one WAV file for one channel, then dump the other square, DPCM & noise channels into another WAV for another channel. I'd then use a sound editor like Audacity or Vegas to combine them as dual-channel stereo.
Otherwise, depending on your tune, you can even do 3 WAVs; one WAV for one channel, another WAV for another channel & the third to cover both channels.
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Technology: the one thing that's hated & cursed at by all engineers, technologists, scientists & technicians!
Well if *I* were you, I would export an NSF of your FTM, then open it in something like NotSoFatso or the like, and isolate each channel and export WAVs of them all in turn. Then I would import them all into a sound-editing program like Audacity and mix them manually to my liking.
(Note that if in the tune you're trying to mix the channels don't all start at the same time in the FTM, then it's useful to insert a dummy frame into your piece that consists of nothing but unison tones in each channel, so that you can more easily line up their waveforms in Audacity when you go to mix them together.)
...But then I'm not you.
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Socrates is a man.
Therefore, all men are Socrates.
Indeed, it is (& that's aside using different effects plug-ins or even integrating into video). I think you can also do that with Audacity, but I'm not totally sure.
As for the matter at hand, it's all about isolating different channels in such a way that they can be spanned across either the left or right channels of a stereo output (or, if you prefer, 5.1 surround sound).
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Technology: the one thing that's hated & cursed at by all engineers, technologists, scientists & technicians!
We've all just said what to do with the WAVs; assign each one to a separate sound channel (according to the right & left ears in stereo, or to the front-left, front-right, front-center, rear-left & rear-right channels in 5.1 surround sound).
It's simple if you understand how stereo, mono & surround work (& as long as you know to export each NES audio channel to either their own WAV files or a handful of combined WAVs).
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Technology: the one thing that's hated & cursed at by all engineers, technologists, scientists & technicians!
Yeah, I know how to do it... but does anyone got any tips on panning and such. I can't seem to get it right. Either there's too much sound in one speaker or there's not enough sound. I can't seem to get it balanced right. Keep in mind, I'm using VRC6 for all my songs. I use two channels for bass (sometimes 3), 2 channels for melody and I only use the triangle channel for toms and such. Noise and DPCM is obviously drums. :P Also, is there any way to make the 8-bit sound clearer? With EQ?
Actually, many good audio editors support pan law in some way; ProTools (the best utility for this, in my opinion,) Cubase, Vegas & to a lesser extent, Audacity.
Pan law's nothing more than the fact that multiple sound waves of equal frequency & phase will compound each other's volume (just as in FamiTracker itself when you play two square waves at the same time).
Mind you, this info will come in handy for me too pretty soon.
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Technology: the one thing that's hated & cursed at by all engineers, technologists, scientists & technicians!
) 
I would love some help.