If you wish to set up your preferred default settings for a particular manuscript or all of the manuscripts in your account, you can do so by clicking on the 3 dots located at the top right:
The Manuscript Defaults, as mentioned at the beginning, are to set up your preferred settings for a particular manuscript, while the Global Defaults are to set up these settings for all the manuscripts in your account. Both contain the same settings, and are very easy to set up and manage.