I think with a self motivated teenager you won't need to worry too much about where to start. At that age he will have the entire software figured out in No time!

your job will just be to remind him to practice!
Show him the games if he hasn't found them already. Show him the Hanon and black and white cats finger excersizes and challenge him to make them fast and even by starting each lesson with a quick run thought them.
Don't start on hot cross buns, but he may like Jingle Bells and even three blind mice. Once he has a couple of simple songs under his belt head for the boogie 1 album. My 9 year old loves the tempo of the songs in this album and I am sure your son will too.
Definitely have him write down ALL his scores. Nothing is more motivating to a teenager than beating a score, especially their own score!
Good luck, keep us posted.