When I first started, I was using garage band, and Neuro programmer. Over time by working with ambient music, I found Ableton Live was a much easier program for what I was trying to do. The rest is history from there. I love using Ableton Live for binaural beats. There are a few tricks to it, but in general, it's a pretty robust program for it. I decided to release a collection of resources in helping others get started with Binaural Beats and Isochronic Tones in Ableton Live.
Here is a free E-book on creating Binaural Beats in Live. I go over the basics of Binaurals and how to edit and create them in Live.
Check out the walk-through video and more at: http://subaqueousmusic.com/binaural_beats/
Get the full Ableton Live Pack at: https://www.subaqueousmusic.com/shop/online-courses/making-binaural-beats-online-course/