[scottz]

Sitting here thinking about it, I think I know what the extra wiring is for. There will be a Hot 1, Hot 2, Neutral (probably two of them) going the the transfer switch. There will also be lead(s) (I don't want to say what colors since I can't verify at this point) that will be connected to the hot lead(s) in the junction box and are used to control the transfer switch (I think I see them behind the L1/L2/N leads in the transfer switch). When the generator starts, the voltage on this extra lead is what makes the transfer switch move to the generator position.