How can i charge 2 3.7v li-ion batteries using 1 power source.

dennis_arduinouser:
Voltage:12V DC
Power(W):2.76

Current=Power/Voltage
I=2.76/12=0.23A

So your fan needs 230mA to run at full speed. So select a boost converter with at least 500mA output capability.

As for the arduino and the motor driver. What exactly is the arduino supposed to do? control the speed of the fan or just turn it on and off or both?

What motor driver are you using? Your arduino is a 3.3V pro mini variant am I right?