You can organise your references into collections and subcollections. A reference can be in several collections. If you delete a collection or remove references from a collection, the references will not be deleted from your Zotero library.
To create a collection: click on the folder button on the left, and enter the collection name. Once a collection is opened, any reference you create or download will be added to this collection. You can also add references to a collection by dragging and dropping them to the collection on the left pane.
To remove a reference from a collection, right-click it and select Remove Item from Collection. To delete a collection, right-click it and select Delete Collection.
To create a subcollection, create a collection and drag and drop it to the parent collection, or right-click on a collection icon and select New Subcollection.
If you want to know the collections a reference has been put in, you can select the reference and click on the Ctrl key (the alt key, if you have a Mac), the collections will appear highlighted.
By default, items added to a subcollection do not appear in the parent collection. If you wish to change this and have recursive collections, go to the menu Edit -> Preferences -> Advanced, and click on the button Config Editor.
Dismiss the warning, type in the search window extensions.zotero.recursiveCollections, and put the value to "true".
To create an automated collection (a collection linked to a search query): use the advanced search function () and enter your search terms, than click on the Save search button. Your search is saved and a collection is created.