How do I have more than one Org-roam directory?

Emacs supports directory-local variables, allowing the value of org-roam-directory to be different in different directories. It does this by checking for a file named .dir-locals.el.

To add support for multiple directories, override the org-roam-directory variable using directory-local variables. This is what .dir-locals.el may contain:

((nil . ((org-roam-directory . "/path/to/alt/org-roam-dir")
         (org-roam-db-location . "/path/to/alt/org-roam-dir/org-roam.db"))))

Note org-roam-directory and org-roam-db-location should be an absolute path, not relative.

Alternatively, use eval if you wish to call functions:

((nil . ((eval . (setq-local
                  org-roam-directory (expand-file-name (locate-dominating-file
                                                        default-directory ".dir-locals.el"))))
         (eval . (setq-local
                  org-roam-db-location (expand-file-name "org-roam.db"
                                                         org-roam-directory))))))

All files within that directory will be treated as their own separate set of Org-roam files. Remember to run org-roam-db-sync from a file within that directory, at least once.