Thats common, the balance ports are wired in a certain sequence and it will know what is connected based on the number of wires that are in the plug. Typically the 6S balance conn can only be plugged in one way so there is no polarity problem. Your charger should recognize what is attached.

It takes the number of cells + one wire to balance, so a 2S balance conn will have 2 + 1 = 3 wires like you observe. Go ahead and plug it in and set the charger up to charger. There should be enough safety checks in the charger that will keep you from setting it up wrong.