You don't need a 5 port EW90 for an internal battery.
If you upgrade from external battery to internal then you need the 3 port EW90 box as that is were the charging port is located, it's seperate from the 3 ports for the actual components.
6870/9070 shifters have 3 ports on them, one for the wire connecting it to the EW90 box, bottom hole for the sprint shifter and the middle one for the climbing switch.
So the add on switches connect to the shifter and then there is a wire from the shifter to the junction box.
So the 3 port box is left shifter(+addition switches), right shifter(+addition switches) and the 3rd port is the wire that enters the frame and heads down to the internal 4 port junction box. This wire, battery, rear mech and front mech fills the 4 ports.
The only reason to get the 5 port EW90 is for the time train extensions as they add another wire each to the front of the bike which can't go into the shifter. It makes it easy for clip on aero bars with DI2 satelite as you just clip the bars on, plug them in and you're good to go. You may need to check all the firmware is all up to date the first time round but after that should be plug and play.