Maybe I am confused, but are you talking about the Lipo battery leads? or the 3 wires for the balancer (on the battery)? You would still connect the batter to the charger with the main wires (larger red and black wires), and if you wanted to also balance the cells at the same time, you would connect the balancer plug also. So if you are charging and balancing the cells you would have all the Lipo connectors attached to your charger.
Let me know if this makes sense, or if I am barking up the wrong tree.