If you used three pairs of connectors you could fit a male and female on the battery and simply bind them together near the base of the connectors with insulation tape or heat shrink tubing as indicated below to ensure they could not be plugged into each other by mistake.
I would use the female connector for the three positive battery connections and the male for the battery negatives and then reverse this for the charger connections
(which should also be bound together to prevent from shorting the charger output).
If the wires for the male and female connectors are coloured the same, I would suggest that you use one colour for each battery so that it would be much easier to check individual battery voltages at the end of a ride using the connectors instead of having to directly access the battery connections or refer to wiring diagrams.
You would still need to make sure that you didn't accidentally plug the charger into the motor connectors
(instead of the battery connectors) as your charger would then be trying to force 12V into the controller with the polarity reversed.
Alan