On notifications page(https://circleci.com/account/notifications), it's possible to set the notification by organizations.
When you can't find your organization on the list (from "Choose an organization"), you may need to follow at least one of the project for the organization - it's not related to the permission of the project on your VCS, but the matter of CircleCI permission. Please make sure you're already following projects from here: https://circleci.com/add-projects/<your vcs (gh or bb)>/<organization name>
Following a project enables a user to subscribe to email notifications for the project build status and adds the project to their CircleCI dashboard. (Reference: https://circleci.com/docs/2.0/projects/#add-projects-page)