Typically the cells in a pack are in series, to get the voltage one needs - that is pretty obvious. But, over time one or more cells charged over just the series connection may not charge up in the same amount of time, leading to an "unbalanced" pack. That cell when used then hits bottom before the others, potentially ruining it. So separate positive leads are also run from each cell, with a common negative, and plugged separately into the charger. Chargers will then monitor the voltage of each cell to ensure they are all at the same level before charging stops. Plain series charging can take a little less time. Balance monitored charging can get a few more mah replaced back into the battery.

Bummer - it seems like Sullivan doesn't offer the 6v any more. I would assume that using a 3S would be fine, although it may pump a bit slower than "normal". It's just a motor and a switch, so shouldn't be very sensitive.