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.
Colored labels make it quick and easy to see certain references. There are 9 colors and these are numbered. Colored labels appear at the top of the labels list in numerical order regardless of whether they are included in the references in the center panel. You can easily color and label references by pressing a number on your keyboard. Right-click a label in the label field and select a color.
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.