I would recommend DevonThink to organize your PDFs and related notes for class. The search is fast & excellent. Use one database for each "set" of documents you want to search together - for example, use one database for each class you're taking.
Use rich text format in DevonThink to take notes. You can paste in images & audio files into a rich text document (Devonthink saves it on disk as RTFD format, which can also be opened in TextEdit).
DevonThink has a neat "create a hyperlink to this page in the PDF" feature, which you can use to build up your notes with one-click access to content inside the PDF. I also wrote an app PDFoo which does the same thing, except it keeps the PDFs in Finder folders, and makes readable URLs. It can also export all your annotations to rich text with pdfoo:// URLs back to the source page in PDF. I also wrote an app PDFExplode to split a long PDF (such as textbooks) into one PDF for each chapter, which is useful when you want search results to be more focused.
You may also like FingerPDF, which collects PDFs and searches across multiple PDFs simultaneously.
You may want to try out Skim.app for annotating PDFs (rather than Preview.) It's faster and has a nice freehand tool for annotations too, in case you have a wacom tablet to mark up PDFs quickly.
Lastly, find a workflow to send handwritten notes to your Mac. I like RemoteSnap app on my iPhone, which allows me to take a photo and immediately sends it to the Mac over wifi network. Devonthink has a designated "Inbox" folder on the Mac, and if you save anything to this folder (such as configuring RemoteSnap to automatically do so) it will get imported into DevonThink. You can also OCR the contents using DevonThink Pro Office version of DevonThink.
IMHO DevonThink is superb for organizing research & learning materials. It's built around the concept of a database though, so if you're more visually oriented (mindmaps and whiteboards) then check out Curio (which I recommend for projects & planning).