You know, we had some internal struggles with that. We originally were going for a bunch of scheduling vs manual publishing options and it got really complicated.
Can you clarify what about it is unintuitive to you? Should there maybe be a way to publish right on the lesson edit page? There is a help doc on 'different ways to run a course' that suggest how you might use that option (https://www.coursecraft.net/help/running-a-course).
