There are a number of ways to organize your Zotero library. Folders are broad tools to compile like items together. Then tags and related items can sort those items even further by the content or other characteristics you choose to use. Notes can be added to a specific resource called an "item note," or thoughts can be added to a "standalone note" that will appear in the library but won't be attached to a specific item.
The "My Library" folder contains all items in your Zotero library. You can create a number of subfolders within the My Library folder by hitting the folder icon (top left-hand corner) and naming a "new collection" (i.e., folder).
Once your folders are set up, you can drag and drop items from the My Library folder into your preferred folder(s). When you add an item to a subfolder, it still remains in the main My Library folder.
When you delete an item from one of your subfolders, it does not delete the item from the main My Library. However, if you delete the item from the main My Library, that item is deleted from all subfolders as well.
You can write notes for any item you add to your Zotero library. Once you select an item, you'll see a notes tab in the right-hand panel. This opens up a basic word-processing document that saves automatically as you type. This space can be used to write notes that summarize the article, describe why that item was added to a particular folder, or list the search strategy and database where you found that item so you can look for other material later. Once you write the note, it will show up as a "child item" under the main entry. You can add citations in your notes to help keep track of resources. This is especially helpful if you reference another item in your item note.
Tags are one way to organize your resources by quickly selecting a term that is assigned to a number of resources in the library. Yellow tags are added automatically by databases (as in the screenshot below), which help identify the contents of the article. You can delete these tags if they are not relevant. To turn off the automatic tag, select "Edit" then "Preferences." Under "General," you can select or deselect the automatic tag option under "Miscellaneous." You can add your own tags by selecting the "add" button. Tags added manually will appear blue.
Nine tags per folder can be assigned a color to help color coordinate a library or make it easier to find commonly used tags, like shown below. To assign a color go to the list of tags in the bottom left-hand corner of your Zotero window and right-click on the tag you would like to assign. A common tag with a color assigned to it is "to be read."
You can link items together by using the related feature. It may be the case that two items are in different subfolders for conceptual reasons, but you may want to link them together because they use the same methodology. You can do this via the related feature. When you click on the title under the "Related" tab, it will automatically bring you to the related item. This will allow you to toggle between the two (or more) related items.