I can’t tell you how much I’ve struggled with this, too.
Keeping in mind that it’s really how you set up a “project” that’s important. In your case, it looks like you set up a project for “Japan Travel Plans” or perhaps “Japan Trip”. Now you have the opportunity to put down notes for that project, right? The “note” shouldn’t be the project, if I’m understanding your use.
If you make “Japan Trip” the project, you could create a note for General plans and notes, and then pin that to the top. Then for your “to do” items I’d suggest one of two approaches:
Approach 1 (All in Agenda)
Create a note for each “to do” item, each having a pegged date. That note might also include other notes or annotations. For instance, your Apply for Visa item, might include the address of where you need to go or any critical information you need. You can then put this note “On the Agenda” and it shows up there as something you need to take care of. When you’re done, you simply collapse and mark the note “done”. This is convenient to do as your “to-do” list grows.
Approach 2 (Hybrid with with Task Manager”
Alternatively, you could use Omnifocus or Todoist (or other Task app) and simply highlight and create a task item in that app. Those would be managed as you normally would (hopefully your task app gives you that ability to create things on your calendar like Todosit, for instance). Then as you complete the task in your Task manage, you check it off in your Agenda note.
I started off doing Approach 2, but gradually have moved to Approach 1. There are drawbakcs to both and positives to both. The biggest issue I have right now either way, is that I am maintaining two systems because I’m also putting everyday task items in my task app, so I have to make sure those get to the calendar. So far, so good. Todoist puts my tasks on the calendar, so does Agenda and both are visible in their respective systems.
Hope this helps. I do believe that the devs at Agenda have said they are partial to giving notes and even “checklist” items more metadata in the future.