The one on the left looks like PAS.
The one in the middle, i don't know. Plug looks like display (5 segments in line) but only two wires..? Maybe battery level indicator.
The one on the right is obviously power.

A charger connects to the batteries, not via the controller. It's okay to charge the batteries whilst the controller is still connected though (obviously it's advisable to switch it off). Really you want this loop... Controller-switch-chargerplug-batteries. So you can switch the supply to the controller off, but the charger plug will be on the battery side of the switch, so the charger will still charge the batteries.