If you're managing a lot of PDFs, I like Papers. It's intended for researchers to manage research papers. I've found it handy for managing other sorts of documents. It lets you specify plenty of metadata, organize documents into collections, and take notes about your documents.
It also sounds like you could use a great primer on using the Finder. Macworld has a bunch of articles to help you learn more about using the Finder, including Finder 101 (which is super-basic) and Mac essentials: files, the Finder, and search (which introduces you to ideas like Smart Folders and lots of things -- it's a long article, but worth the time investment). Macworld has lots of other resources. Your question is pretty broad; if you update, I might be able to provide some more specific recommendations.