I think I'm following you. I get the Neve now (I apprenticed as an audio engineer in high school :)
Binaural beats don't work so well in mp3 format -- the way mp3 compresses is by getting rid of information that is not audible, and if you mask the binaural beats in music, the beats will probably mostly be eliminated. So, you may have to use a lossless format rather than mp3.
If you blink the LEDs to the music, you want to make sure that they are still blinking at brainwave frequencies, ortherwise they won't be helping your brain synch up to the programmed sequence. So, maybe you could modulate the brainwave sequence with the audio input, fading the blinking in and out according to the music's amplitude? Or, maybe just blow off the brainwave info for the lights and blink them according to the music, using colored lights for a really nice light show as the binaural beats are doing their thing.
But if you are using your really nice audio equipment, you can generate your own audio for the binaural beats and come up with something that sounds way cooler than the low-pass-filtered square waves this simple Brain Machine produces. The Brain Machine firmware (which is free and open-source) can be downloaded from my website:http://www.CornfieldElectronics.com
(click on the "maker faire" tab)
and it gives the meditation sequence in the table at the beginning of the "slm.c" file. From that you can generate your own audio for binaural beats (using CoolEdit, or any other audio software).
Does all this make sense?