By default, BackHub creates backups of all repositories for which it has access. When you give access to all repositories during the installation process, backups for all current and future repositories in the associated GitHub account will be automatically created.
BackHub checks your GitHub account for new repositories on a daily basis. If a new repository is found, a new backup is created. As more backups for private repositories are created and you reach the limit of your plan, BackHub will remind you to upgrade your plan through GitHub Martketplace to avoid interruption of service.
See also the FAQ.