Do not hijack an existing thread. Always start a new one when you have a new question.
The AAC Ebook section on transformers - http://www.allaboutcircuits.com/vol_2/chpt_9/4.html - should answer your question. Since the transformer is an AC device, I am sure you realize that the polarity changes with each cycle.
Connect your voltmeter black lead to the junction point CT which is the center tap.
Probe each cell opposite end with the voltmeter red probe. One will be positive and the other negative with respect to the center tap.
On a transformer, same polarity difference shows but alternating many times per second.