Sorry, I missed this...
Ypedal is right. The connectors on the other side are for using these with smaller battrey configurations. They aren't used here. The harness connects the balancers to each of the cell connections via the 18-pin connector on the front of the pack. The balancers work independently from the charger, so there's no direct connection.
The larger gauge wires, which ternminate in the Deans connector (These are used a lot in RC applications. I like them because they are small, but can handle 100A.) are the main pack discharge leads. The negative lead is routed through two 4110 FETs on the LVC board. The smaller gauge wires, with the PP connectors, are for the charger. The only difference is that the negative lead goes directly to the negative pack lead.
The charger works great for LiFePO4-based packs. It has adjustments for both voltage and current and what I did was max the current out at about 4.5A and adjusted the voltage so that the cutoff was about 59V, which works out to about 3.69V per cell.
It has been my experience that these LiFeBatt cells really don't get too far out-of-balance at all, but since you will be using them at higher current limits, I'd still use the balancers about every 5-6 cycles. What you want to do is plug the charger in, wait until the green LED comes on, which indicates it is in the final CV phase, where it drops the current to 1A and holds the voltage to 59V. You will see the current on the WattsUp meter start to slowly drop. When it gets down to 100mA, or so, you can turn off the charger and plug in the balancers and then go away for an hour, or so. Eventually, al the LEDs will blink in a randaom fashion, which means the cells are all pretty close. If you leave them connected long enough, all the LEDs will go off, which indicates that the cells are all within about .005V of each other, but I think this is overkill. Mainly, you just want to make sure the cells are all in the same ball park.
-- Gary