RE: Airplanes for dummies.
It depends on the charger. If you get a more expensive balancing charger, you'll connect it to the white connector. I'm using a cheaper charger that connects to the Deans connector (a big blocky connector with just two wires that's pretty common for batteries nowadays) and charges all three batteries simultaneously. It's ok to charge the battery using the two-wire connector, especially when they're new. Over time, if you don't balance the batteries, you won't get a full charge out of them because one of the cells might not be fully charged.
I'm no expert on batteries, so if someone more knowledgeable wants to speak up, please do.