I really miss the functionality of the older version. Where i could leave Note Annotations and view them as a list on the Right panel - to navigate through my thoughts inside files.
It's still there. You can view annotations in the Annotations tab of the left sidebar and take notes and add annotations to notes in the Notes tab of the right sidebar.
Upgrade Storage
This is probably what you are looking for:
https://s3.amazonaws.com/zotero.org/images/forums/u265723/jzmjntw949okni6c2n9h.png