1.) Out of famitracker do you guys split the wav's into separate wav's for each channel, or keep it as one wav file out?

It depends on the context of how I'm going to process it and whether or not I want the result to end up in stereo.

2.) What sort of EQ and processing (if any) do you put on the tracks?

Depends on context, usually compression to make the attacks articulate. Sometimes light reverb or delay to give the impression that something is playing inside a room.

3.) Any tips for EQing triangle / sawtooth?

Also depends on context, but, as little as possible. Maybe roll lows off if there are issues at that end.

I think there was a thread about this already.

1.) Out of famitracker do you guys split the wav's into separate wav's for each channel, or keep it as one wav file out?

2.) What sort of EQ and processing (if any) do you put on the tracks?

3.) Any tips for EQing triangle / sawtooth?

You should be able to plug in another known audio source that sounds LOUD and play itback to a result that is also LOUD. That's the beginning of getting a good result  the software and gear are beside the point otherwise.

Invest in a proper soundcard. Most integrated ones are no good for recording.

This.

yeah, try to evolve away from using a microphone. Direct sound from the jack is what you need to eventually be doing.

No, I am using the jack. That's just how terrible it is!