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

Yes there another way. Use just One charging board and One battery, then use a small DC-DC step up (boost converter) to take 3.7v input to give you a 12v output and the fan will run at full speed.

I presume the fan you're using is a brushless pc cooling fan that consumes below 200mA