You don't necessarily have to push all files into the global agenda. Instead, you can set `org-agenda-custom-commands` to something like

  '(("p" "Some project"
     ((alltodo ""))
     ((org-agenda-files '("path/to/file.org"
                          "path/to/another.org"))))
    ("o" "Another project"
     ((alltodo ""))
     ((org-agenda-files '("another/project/file.org")))))

Now using `M-x org-agenda p` will give you a todo list for the first project, and `M-x org-agenda o` for the second project.