Aloha despinamccoy,
1. You can breath in a natural, relaxed, and even way during your active exercises or sitting meditations. The "reverse" breathing is a Taoist technique that Chunyi has found to promote healing faster. You will read all sorts of things on the web and books by various authors regarding the technique.
I suggest choosing a system/teacher and following his or her guidance. Since it seems you've chosen Master Lin and the Spring Forest System, then do the breathing as he suggest. You can slowly work you way into it, but doing the reverse breathing during the three deep breaths at the beginning of your exercise and continue with regular breathing through the rest. After a while you may find yourself reverse breathing automatically during your practice.
2. You can start doing the Level Two healing steps on others right away. The active exercises can be integrated after you have made a shift physically in your system with the Level One active exercises.
His Levels One and Two are available in a home study course format. Levels Three and Four are presented in an in-person classes or retreat setting.
Much Love, Shawn