Ok, I've installed maybe 6 or 7 sets in the last year. A couple of them with the "traditional" cabling with the cables only under about 5 bar tape turns and the rest with under the tape all the way.
I prefer the under the tape complete. I run the shift outer under the bar until the upturn then move it to the inside of the bar, up past the brake levers where I set both outers into the same front groove in the handlebar.
I've tried crossing the shift cables and running them on the correct sides. Putting them on the correct sides seems to have a cleaner inner cable run while reversing the outers and then crossing the inners on the way down to the BB routing seems a little better for the outers not to rub the paint off of the head tube.
However, as you've been informed, you'll have to run a tandem rear cable. The longest standard cable (Campy which is also the best) is about 3" too short.
I find that really irritating since 4" of cable cost nothing to the manufacturer and he gets so little advantage to it that you'd think it not worth their while to get all of the bad vibes.
I can now put the setup together in about 30 minutes.