No, Zotero isn't designed to work that way. It may help to reframe how you think about your folders. Zotero can put files in a given folder for you, but you generally don't want to manually add files from a given folder to Zotero.

In Zotero, you generally add items from the web, which downloads metadata and saves a PDF if available, storing the file in its own storage.

If you only have a PDF on disk — say, because you received it via email — you can drag it to Zotero, which will try to retrieve metadata for it. You can then delete the original copy on disk.

If you want to store your PDFs in a particular folder (e.g., "Literature"), you use linked files, generally with the help of the ZotFile extension, which will convert the default stored files into linked files in a location of your choosing. (You can manually create linked files in Zotero, which it sounds like maybe what you've been doing, but that's tedious and not really a recommended workflow.) If you have a file on disk that you're adding to Zotero, it would generally be in a temporary folder such as a download folder, and you would drag it to Zotero — resulting in either a stored file or a linked file in a configured directory — and then delete it. You shouldn't spend time manually putting files in folders when Zotero can do that for you.