I pretty much have a different system of organising myself for every subject:
English - Each different text has its own display folder, and then I write on lined paper. They end up pretty thick, but I bought the better quality ones with more sleeves, so its allright.
Maths - exercise book with a 2-ring binder for handouts/past exams and tests, etc.
Ancient History - lever arch file with all of the different topics seperated by dividers.
Religion - exercise book
PE - Lever arch file
Bio - same as english, with a new folder for each different topic
As for studying, I'm one to only study for assessments, and study for exams with only a week, week and a half to go. For Ancient History, Bio, Maths I have those books with all of the past exam questions seperated by topic, so I use those to study with.
I'm one to write copious amounts of notes as well, just so the information sinks in. This is why I also do heaps of practice essays, so that I can look at different ways of applying what I know, and then I won't get caught out in an exam situation where they really can ask you anything.
For maths in particular, do as many questions as you can, and not only learn the formula, but learn how to apply it in as many different situations as you can.
I hope that was helpful, good luck!
