Well one of reasons the A123/LiFe batteries might have a two wire lead and a three wire lead, is balance charging.
The two wire lead would be for discharging or powering the model, the three wire lead will typically use the signal wire as a balance lead for charging. On the Spektrum/JR 2.4GHz radios, if you plug that three wire lead into the rx and then try to bind the rx, you'll let the magic smoke out of the rx....
Best to do a bit more research on what you have for a configuration of the wiring as there are a number of ways to do things with three wire HD switches and these batteries.