People coming from other tools based around a “watch folder” sometimes look for similar functionality in Zotero and are surprised to find it doesn't exist.
Zotero is designed around a different workflow from these other tools, and it reflects a bit of a philosophical difference. We don't believe you should have to manually download files and worry about folder paths. Zotero is deeply integrated into the browser where you do most of your research, and it has an unmatched ability to save high-quality metadata from across the web.
To save to Zotero, you simply click the save button while on an article page, and Zotero will both save bibliographic details for the item and automatically download a PDF if one is available.
If only a PDF is available, you can still save it directly with the save button, and Zotero will attempt to retrieve metadata. Make sure your browser is set to preview PDFs in the browser (at a ''http://'' or ''https://'' URL) rather than download them and show them at a ''file://'' URL, which the Zotero Connector can't access.
If you already have a local file on disk (say, from an email), you can drag it to the Zotero app, but that's not the primary way of adding items.
Once you've saved an item, Zotero manages your files for you, including renaming them based on the author, year, and title of the parent item and, if you use file syncing, making sure they stay linked across devices. There are plugins that can help you organize your files differently if you prefer, but file management is still done automatically for you based on your settings, not something you have to manage manually.
Ultimately, Zotero is designed to save time, and we try hard not to implement features that we believe encourage more tedious workflows. Since Zotero is open source, most things can be done with settings or plugins, but our goal is to create a default experience that just works for most people: one-click saves of data and files, automatic file management and syncing, advanced in-app organization and searching. Give it a try!
Still not convinced? Read through Adding Items to Zotero to better understand all the various ways of getting data and files into Zotero, and post to the Zotero Forums with other questions or comments. We're always happy to talk about our design decisions there, and we can often recommend a better way of doing something if you're having trouble.