Negative (black) probe onto the black wire and the red (positive) onto the one next to it. That will give you the reading for the first cell. For the next cells just move both probes over by one. Easy, just make sure that your probes don't make contact with each other while you are taking measurements as you will more than likely fry the balancing wires.
By the way let us know what state your lipos were in. I would be interested to hear how they held up during all that time.