There are a number of ways to organize your Zotero library.
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. You might want 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.
Some 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 you want. You can also add your own tags by selecting the "add" button.
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.