When you are trying to get your arms around how Di2 wire kits work, it is best to think of the wire kits in terms of front and rear meaning, one wire kit for the front of the bike and one wire kit for the rear of the bike. If you could imagine looking at the profile of a bike and drawing an imaginary line right down the center, you would have a wire kit for the front half and a rear wire kit for the rear half. There is no longer right and left like standard cabled and housed mechanical shifting bikes.
The front wire kit has a center junction box. This junction box has three wires, one for each shifter and one the travels down the down tube to attach to the rear wire kit. No sizes to choose from with the front wire kit - one size fits all frames.
This junction box Shimano actually refers to as Junction Box A. Other than serving as a router for the three cables, it features a battery charge indicator and flashes when the battery charge reaches eight hours or less. Junction Box A is also involved in adjusting and fine tuning the derailleur adjustment.