The intended assembly is a Junction Box B around the crank area and a Junction Box A around the cockpit area. With that, it should be straightforward to measure on the outside of the frame and add a bit for safety.

As far as I can tell, as long as the components are connected in some way or another, you're good.

NBs:
- the shifters on 6870 have three ports each (it's possible one is reserved for satellite shifters, though)
- you probably want the internal battery in your seatpost, in which case you probably want to have enough wire to pull the seatpost out and disconnect the Di2 outside the frame

Personally, I run a 1200mm from the B directly to the A in the handlebar end (2-port), then a 350mm to the nearest shifter, and probably a 650mm from there across to the other shifter. If I remember correctly, I use an 850mm wire for the battery. The FD is on a 350mm wire and I can't remember the RD specifics. I do not use D-Fly.

EDIT: 58cm frame; 12cm stem; 44cm handlebars.