Electronic & Hydraulic Shifting (Di2, Ui2, customisations)

Will the internal battery fit in my Trek Domane?
Do I want the USB charger or not?
3 port or 5 port on the junction box?

It fits inside a Cervelo S2, so I'd be very surprised if it didn't fit in a Domane.
Yes, you do.
3 port for a road bike, 5 port for a TT bike.