Mark, you are doing well so far.
A. Follow Mary's advice. As far as I know, there is no way to have one self-enrollment to every course in Moodle. I think self-enrollment is course-by-course. I was not sure if your question was about yourself, the Manager, having access to every course, or if you want students to log in once and have access to every course. In my case, for each of my courses, I use self-enrollment. I set up an enrollment key, email this to students, and then have them access their course. If they happen to be in two of my courses, I have to send them two enrollment keys, one for each course.
B. The look for a Moodle is very flexible but takes some time to learn and set up. Moodle.org's theme is a custom theme that only moodle.org wants to use, so it is not available to you. You have the Boost theme, and without too much effort, can change its appearance. I gave a presentation at MoodleMoot last year about what I do. See: MoodleMoot2017 (US and Mountain), "Making Boost do MORE".