Charging (via USB) and using 2 Li-Ion batteries in parallel simultaneously?
There is a major question here, how much current does the load pull from the batteries?

To charge a set of batteries properly the charger has to provide enough current to satisfy the load and to charge the batteries at the same time. If your load pulls 100mA and your batteries want 200mA of charge current then it's pretty easy. Microchip makes charge controllers MCP73812 for example. Two batteries in parallel balance each other and don't require additional balancing. This setup can also be supported on a regular USB port that can supply up to 500mA with enumeration. An FT230X FTDI chip could be used to enumerate and juice the bus to full current. 

If you load current plus charge current are greater than 500mA then a wall charger is needed. This means that you won't be able to charge from a computer and only specific high current charges would work. Microchip makes charge controllers for this too MCP73861 for example. (double check the chip voltage is compatible with your battery voltage)