Part of the beauty of Agenda is that you can change your mind! You can consolidate multiple projects into one, or split one project into many. So my suggestion is to go with whatever feels right to you now, and then adjust as you get more experience with it.
Some of my approach and experience follows:
I typically start with fewer projects, and then split things out into more projects when I feel that it’s needed. I also like to have one note correspond to one calendar event. You mentioned “a new note for each item” so I’m curious if by “item” you meant “calendar event” or “item to discuss.”
Anyway my approach seems to have settled closely to the “next box” concept that is at Agenda’s origin.
I keep a pinned note for things to discuss, and add things to it as they come up. I also keep an ongoing record of important information in that note. When I do my final preparation for a meeting (day before, day of, right as it’s starting…) I’ll copy the relevant items from the pinned note into a note linked to that meeting. The items are all checkboxes, and I check items off as we discuss them. I type ----- as a separator after the checkboxes and record any notes from the meeting there.
When the meeting is done, I update the pinned note based on what happened during the meeting. If I want items to be part of the ongoing record, I check them off in the pinned note. If I don’t care to keep that information top-of-mind I just delete those items from the pinned note (keeping in mind they’re still recorded in the specific meeting note). I clean up the meeting note, and incorporate any relevant new notes from the meeting into my pinned note.
So that’s the basics of it. I use undated pinned notes as a primary consolidated reference, and unpinned dated notes for ephemeral data specific meetings, and copy information between them.
What eventually happens is that I create multiple pinned notes in a single project (“things to talk about at this meeting / with this person” and “things to talk about at that meeting / with that other person”), and I find that when looking at a project I skip over a bunch of notes or search for things. At that point I break things out into separate projects.