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.) The collections containing the item are also identified in the Libraries and Collections section of the Item details pane..
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.
Tags
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 pane when the item is selected. Tags can be edited in both locations. To prevent tags from being imported with items, go to the General section of Zotero settings 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.
Notes
To create a note attached to an item, select the item from the list in the center column and either click the New Note icon at the top of the center pane(
) and select New Item Note, or go to the Notes section in the Item pane and click on the + sign.
A note will be created as an attachment to the item the note editor will appear in the Item pane. 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 Reader tab in this guide for information on creating notes from annotations in your PDFs and EPUBs.
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.
Related
Items in your library can be linked to each other by marking them as related. In the Related section of the item details pane, click on the + sign. Browse for and select another item in your library. Selecting the item marks both items as related to one another. Clicking on an item listed under Related allows you to navigate between the items. You might use this to relate a primary source to a book chapter that mentions it, or to relate a book review to the book it reviews. (Note, using Zutilo, you can easily relate multiple items simultaneously.)