Your workflow sounds fine to me.
There is not really one way to use the app. It depends on the “granularity” of your projects as to what is best. For example, if you were finding that your notes for each project you have were getting really long and ungainly, you might consider making the real life project into an Agenda project, and splitting that really big note over several notes (eg one per week, one per sub-topic etc).
But if you find your notes are workable with the current setup, I think your approach is the right one.