You can sort your sources after import by dragging and dropping them into various collections and sub-collections. If you do not import your sources into a specific collection, they will be located in "Unfilled Items" until you sort them:
You can also organize sources by tagging in Zotero. Assigning different sources a single tag will allow you to easily retrieve all sources with that tag by simply clicking the tag. Tagging can be a great way way to distinguish sources by topic, but it can also be used to set up workflow functions in Zotero.
To Tag a Source, select the source and select "Tags" in the right info panel, then click "Add" and type your new tag in the box:
You can browse and search your tags using the Tag View box in the lower left of the Zotero Client. Click on any tag to bring up all articles associated with it:
Zotero will auto-tag sources on import based on keywords and subject headings. These are often not terribly useful or easy to navigate, so if you plan on using tags for organization it can be a good idea to disable auto-tagging. To disable auto-tagging, go to Tools > Preferences > General and deselect "Automatically tag items with keywords and subject headings:"
You have complete freedom to organize your collections and sub-collections however you like. Some ideas for organization include:
You can also use Zotero’s collections feature to structure your research workflow. For example, you can import citations into the main collection folder or into Zotero’s “unfiled” folder, then only sort them into subfolders after you’ve have read them. This can help you keep tabs on which sources you have read, and which you have yet to read. You can then use tags or additional sub-collections to indicate which articles you’ve finished taking notes on, which you’ve decided to use in your own writing, and which you’ve completed citing.
Ultimately, there is no one right way to organize your workflow. What matters most is consistency!