You can use a tl431 and a P-mosfet as lowvoltage detector and shutdown controller, i made a LiIon hack for my bosch powertool: Under spændings detektor med tl431 bruges til Li Ion hack af bosch skruemaskine – Vertikal Integration
I Just connect a standard cheap RC multi charger like this: Multilader fundet på ebay.co.uk – Vertikal Integration
Also, there are IC able to handle multible batterier. A great arduino project could be to make a LiIon/LiPo charger for 20 x cells 