When one of the cell light is red and bliping, it means there is a problem with that cell right ?

How do you balance the battery then, do you just press the start button in the balancer and you leave it alone until it does it's job?

3cell 11.1 volt battery BTW.

I just always connected it to my TP charger and left it alone. But now 1 of my batteries after the charge was showing a red light on the 3rd cell. Should I just leave the battery on the balancer alone and wait ?

just let it do it's thing , the single blinking light is the cell that's out of balance and it's working on it. some times it can take a while if way out of balance. The easiest way to balance a thunder power battey is use it while charging the battery