At first I thought it would be a better idea that when one battery dies, to unplug the battery wires from the HUZZAH and plug them into the other battery. But since it is more difficult than anticipated I added wires so that the HUZZAH will be plugged into both batteries at the same time. I just need to be extra careful to not turn both on at the same time. I also extended the battery wires so that they are easier to unplug/plug in. I also extended the wires on my Adafruit lipo charger. Hopefully in the future all of these modifications make it easier to charge the batteries.
Still chugging away at the second piece. I've chosen a bedtrack for each of the colours, red, green, blue, and yellow. I don't think I'll do purple or orange. I've also decided on what audio processes to use for the green, red, and blue. Now I just need to figure things out for the yellow. I chose Bees for the yellow bedtrack and it's proving tricky to figure out what I can do with it that sounds good.
If you are looking for a summary for my Masters thesis, it is here.