Batteries connected in parallel (positive to positive, negative to negative) are seen by the charger as one large battery of the combined amp hour capacity of all the batteries. Thus, three 12 volt 100 amp hour (ah) batteries in parallel are seen as one 12 volt 300 ah battery. They can be charged with one positive and negative connection from one charger of the recommended amp output. They also can be charged with a multiple output charger, like a three bank unit in this case, with each battery getting its own connection at battery voltage. The charging amperage would be the sum of the individual output amps.
Batteries connected in series are a different story. Three 12 volt 100 amp hour batteries connected in a series string (positive to negative, positive to negative, positive to negative) would make a 36 volt 100 ah battery pack. This can be charged across the pack with a 36 volt output charger of the appropriate amp output. They also can be charged with a multiple output charger, like a three bank unit in this case, with each battery getting its own connection at battery voltage (12 volts in this case). Either method is fine, UNLESS one or more of the batteries are tapped at lower than system voltage. An example would be tapping one of the batteries in this 36 volt string at 12 volts for a radio or some lights, etc. This imbalances the pack, and charging at system voltage (36V) doesn't correct the imbalance. The multiple bank charger connecting to each battery is the correct way to deal with this series battery string, as it corrects the imbalance with every charge cycle.