Saving of files

I am new to Zotero and am trying to organize my downloaded files...but I am a bit confused about how things are saved and copied. I can see the same items in "My library" as well as in the sub-collections of "My Library." Is this how they are stored or are they duplicates? Ultimately I would like for "My Library" to show that there are no files, all files having been moved to sub-folders. Is this possible, or do items show up in both places?
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