You can surely use the Thunderpower charger for the little 7.4V 2S batteries. But make REALLY sure you set it to the right current (amperage and voltage) .
It's quite a bit lower than most batteries you'll use for your other heli's .

But you can't use your balancer, as its for 3 and 4 cell LiPo's if i'm correct. My guess it won't balance correctly with one less cell connected, as it'll read a major imbalance and will only try to 'charge' the 'empty' cell. At least, that's what i think .

Why not use the stock charger? Works perfectly fine and keeps them fairly balanced too!