I have taken a rather circuitous approaches to robot charging and power source management for this project. 5v and 8-9v power is supplied and regulated by a custom board that utilizes four spdt relays to switch the power source from 2x 6600 Mah 4.2V lithium ion battery in series to an external source that charges the batteries in parallel and supplies powers. A 2.5F cap acts as a 5v supply "ups" to ensure the raspberry pi continues uninterrupted when switching. This board utilizes a depreciated Adafruit lithium polymer dc charger (MCP73861) and a hobby 5v ubec. It provides 3x 8-9v supply , 3x 5v supply, and pinouts for charging status, external power supply status and relay switching.

Schematic and Board (power.sch & power.brd)