In this podcast, JJ talks about how the 3 stages of training actually show up in every exercise we do, every time we ride. Being able to adjust the dials and correctly gymnastize your horse while keeping these 3 stages in mind not only helps your horse gain the strength and skill to go up the levels, it also stops what we often call "training holes" from ever becoming a deep-rooted problem that needs to be addressed after they've taken hold.
The 2 books JJ references are The Athletic Development of the Horse, and Dressage Principles Illuminated both
by Charles de Kunffy.