^^^GREAT book^^^
In breeding, you should be working with populations of a thousand or more individuals, and flowering them out to look at traits in all life stages- seedling vigor, structure, flower traits, etc- and choosing which ones to continue. With auto strains, since you can't reserve a clone of each as a backup, this becomes even more important, and keeping track of the genetic heritage of each individual in a breeding program.
One thing for sure is that the parents you choose to create your seed line must both be homozygoous for the autoflowering trait. I don't recommend it as a goal for new growers; easier traits to breed for are structure and finish time.