Firstly, the charger has the balance tap wires that allows the charger to monitor the battery on the individual cell level. When one cell gets overcharged, the battery then starts discharging a trickle of power from that high cell, while at the same time lowering the amps flowing into the whole pack. Eventually, if it's not to out of whack, the low cells catch up with the high ones.
On a large pack, by connecting the balance wire harness in paralell with another pack, the charge level of one paralell cell will try to match the other, like water seeking it's level in two cups connected by a tube.
With some lipo chargers, the balancing won't work as well with paralelled packs, because the ability of the charger to discharge the high cell gets to be too small. So balancing a 20 ah paralelled pack on a 50 watt charger is not going to work as well as a hyperion charger built to balance a pack faster.