I am not a lithium battery expert. I did some reading on bottom balancing versus top balancing (BMS). I choose the simpler solution since it's just a golf cart and max range every time driving wasn't an issue.
From what I gathered I bottom balance the pack to a bottom starting point for the batteries before charging. They all charge at different rates so some will get to their max before the others. You cannot do doth, bottom and top balance, it's one or the other. Bottom is cheaper and only is done once.
Go here and read as much as you can. I did.
http://www.diyelectriccar.com/forums/
The yamaha got the exact same big pack as the ezgo did. I only separated it for easier mounting. If I was to do it again and didn't need 40+ mile range I would just use half that big pack.