Everything added to the Zotero library appears in "My Library." You can create collections corresponding to your projects by clicking on above the Library pane. You can add sub-collections within collections.
If you have a collection selected when you are importing items into your library, the items will appear both in "My Library" and in the collection you have selected. These are not folders you are sorting your citations into. It is better to think of them as iTunes playlists, where the original lives in the library and the song information is added to a playlist xml file. When you remove an item from a collection, it will not be removed from "My Library." If you send an item to Trash, it will be deleted from any collection it was added to and from "My Library."
To add items to collections, select them in "My Library" and drag them into the collection. The same item can simultaneously exist in multiple collections. To see which collections includes an item, select the item and then hold down the Option (Mac), Control (Windows), or Alt (Linux) key. The collections will be highlighted in yellow. (This does not work in Group Libraries.)
In addition to storing bibliographic information, Zotero can save links to the full text, full text attachments, tags for organizing your content, snapshots of pages, notes about the items, and also stand-alone notes.
When you import items from databases, the subject descriptors attached to the items may be imported as tags. You can edit them, delete them, or add your own tags to each item. All tags are displayed in the bottom of the left column and the tags for each item are displayed in the item details column when the item is selected. Tags can be edited in both locations. To prevent tags from being imported with items, go to the General tab of the Zotero preferences and uncheck "Automatically tag items with keywords and subject headings."
By default, the Tag Selector in the left column shows all tags present in the currently selected library or collection. As an alternative way of adding tags, you can drag one or multiple items (or files, links, and notes) from the center column and drop them onto a tag in the Tag Selector.
To create a note attached to an item, select the item from the list in the center column and either click the “New Note” button at the top of the center column () and select “Add Child Note”, or go to the “Notes” tab in the right-hand column and click the “Add” button.
A note will be created as an attachment to the item (it will also show up under the “Notes” tab), and a note editor will appear in the right-hand column. You can create a dedicated window for the editor by clicking the three dots in the upper right and choosing “Edit in a separate window.” Text in notes is saved as you type.
Zotero will sometimes automatically import information from a resource, such as a table of contents or abstract, into the notes of an item. Use the editor to change these. Or right click on the attachment in the items pane and send it to trash.
See the "Zotero's PDF Reader" tab in this guide for information on creating notes from annotations in your PDFs.
Standalone notes are not directly related to any item in your library, and will appear in the list of items in your library. To create a standalone note, click the “New Note” button and select “New Standalone Note”.
In the General tab of the Zotero preferences, you can choose to automatically take snapshots of web pages and automatically attach associated PDFs (when available) when importing references. These appear as child items attached to the items listed in the middle pane. You can choose in preferences to have Zotero automatically rename attachment files using the parent metadata. If this does not happen automatically, right-click (ctrl-click for Mac) on the file name and choose "Rename File from Parent Metadata.".
You can attach files manually by dragging a PDF (or other file) into the middle pane. Dropping a file into your collection will copy it into your library as a standalone item. Dropping it onto an existing item will attach it to that item.