With Zotero you can add a library folder so you can organize you reference into its catagory. How do you organize that it is totally you who decide. For example, you can make folder based on the subject or your reference and put all related references in that subject folder. People may also create folders based on the type of the reference such as books, journal articles, reviews, conference proceedings, etc. You can choose how to do this the most convenient way you think.
To add a library folder,...