Any notes (as well as files) you save can be quickly accessed from the item itself in the center column. Just toggle the arrow to the left of the item to reveal any attached notes or files.
The most important tip I can offer about troubleshooting is to have you read Zotero's instructions on backing up your data. No matter what issues you may run into with your data, if you understand how to create a backup, all will be well.
Additionally, Zotero offers a nice checklist of troubleshooting tips to try when all else fails: https://www.zotero.org/support/troubleshooting_translator_issues.
It seems like a great idea to check the box to "enable proxy redirection," but it's really not. Especially if you do research at several universities, this option can cause problems and general proxy confusion. Zotero may also attempt to proxy resources (like WorldCat), that should never be proxied. Proxy preferences are now located in the Zotero browser connectors. Just right-click to display your options:
and uncheck the "Enable proxy redirection" setting: