I've seen people do both successfully. It plays fine alongside existing non-linked org files. I personally have ~/org with my preexisting files, todos, etc at t

I've seen people do both successfully. It plays fine alongside existing non-linked org files. I personally have ~/org with my preexisting files, todos, etc at the top level and (setq org-roam-directory "~/org/roam") as its own thing to try to make it easier to clean up if I decide I don't like it after all. Having a good time so far though.