It is more complex to have a balancing charger, as required for two cells, and the charger may not correctly deal with the situation where the circuitry is on while the charger is charging (a concern with all hobby LiPo charging modules).
The "3PDT" (3 pole double throw) manual switch is Adafruit's answer to this problem: you can't use the cells while they are charging.
Given the expensive destruction associated with overcharging and overdischarging Li-based cells, you are much better off with NiMH cells. 3xAA will provide 3.6 V nominal with 2500 mAh capacity, can be trickle charged continuously, and are far more tolerant of abuse.