Re folder structure, you can just select the co.noteplan.NotePlan3 application folder and everything will be included in Obsidian. The Calendar folder will contain your daily notes, which you can target by modifying the plugin settings Date format to YYYYMMDD, then the Notes folder will contain everything else. The bonus of this is it means Obsidian system files like obsidian.css won’t appear in NotePlan.
To make this even cleaner, we need an update that allows you to hide folders from Obsidian, so that we can hide NotePlan’s system folders. If you want that too, upvote this feature request! Hide select vault folders from Obsidian