There are many ways to keep your library clean and tidy, for example by creating folders and tags.
1. Create and organise folders
Create a New collection and organise your items using folders (which Zotero calls "collections"). Drag and drop to re-organise.
2. Duplicate items
This is where you find your duplicates. Choose the item you wish to be the master item and tick Merge 2 items. From the popup window, you can also choose which metadata you want to retain in the item which is kept, by selecting the relevant field.
3. Unfiled items
In this file the items not yet sorted into folders are placed. Go through the list and see if you can place them in a pre-existing folder.
Notes are a good way to add personal thoughts and information to the items stored in your library. All notes will also be searchable in your library. There are two types of notes:
You can add tags to all the items in your library; some items already have some tags when you import them. Tags are a great way to make your items easy to find when your library grows large.
Zotero can function as a PDF manager. It can download PDF files together with item metadata, and you can find the files and search their contents in Zotero. However, if you use Zotero as a PDF library your free 300 MB storage will shrink quite rapidly.
In order to enable or prevent Zotero from automatically attaching PDF files when importing an item, go to Zotero Preferences → General → File handling > tick/untick Automatically attach associated PDFs […].
If saving files in Zotero, it might be a good idea to check your storage.