How to use LBO on Powerboost 1000C as input for Arduino
Ok so I went into the Adafruit discord and found the answer. Its a bit hacky but here it is. Solder a wire to the pin that is alone on the onboard transistor. (the only transistor on the board, which is right above the Bat and Vs pins). Then connect the wire through a series resistor (100-10K worked for me) directly to the digital pin.

Then in code if the pin is HIGH, the battery is low.