I’m having a similar issue and tried what you suggest above, but unfortunately, you can only use iCloud drive with your primary account on a Mac, not multiple.
I am logged into iCloud on my work Macbook Pro using my work creds in the System Preferences because I need to for work. I also have my personal iCloud account logged in as a secondary account on the same computer, but as mentioned, one cannot us iCloud Drive for a secondary account.
I get that the limitation here for syncing is Apple and their decision to have one iCloud drive account per device, but also, Agenda made the decision to use this platform.
I do like Agenda thus far, but for me to sync my notes in Agenda, it seems like I would need make significant changes to my personal iCloud setup. This seems pretty extreme.
As there are a few threads here about syncing and this issue, is there any chance this is being looked at?