Great questions about Echinacea. Generally speaking the flowers of Purple Cone Flower (Echinacea purpurea) are used similarly to the root although much less potent than the roots. However, the flowers are a great option for medicine while waiting for the roots to establish. You can make tea or tincture of the flowers and use it much like you would the root.
For the approach of the course. Ultimately that is entirely up to you and how you might want to do it, since you can watch classes in any order you wish. I recommend playing through the classes in order as the information does build on itself a little bit and the quizzes are related to what you just learned in each course. Then use your handbook as a reference to read more deeply about certain aspects of the video class.
Choose the plants you wish to work with whenever you like. One or two might stand out to you as you are learning about them, or you may want to finish the class before reviewing the options to choose. Or you may see a plant while you are out and about that calls to you and you can start to research and learn about this by yourself!