What voltage are they set up to run off now? If they're only set up to run off two cells, then going to three directly will cause more than just additional brightness- it'll most likely cook them. Their current draw spikes up sharply when you go a bit past their normal running voltage (usually like 3-4V for most of the ones we use).
To run them off two of the three cells, just connect them to pin #1 and pin #3, or pin #2 and pin #4. They'll obviously only let current flow if you get the polarity right. The red balance tap wire is usually connected directly to the positive pack lead, and the black is usually connected directly to the negative lead, and then each adjacent pair of wires (1+2, 2+3, 3+4) will connect to one cell. (Thinks): "I wish I had a picture to explain it better"... Ah, wait: Google to the rescue: