Re: best way to organise books?
This is what I do. It suits me, but may not suit everyone else.
Ancient History/PDHPE: Each have their own lever arch folder, with dividers seperating work as required, write on loose leaf paper.
Maths: I have a 2-ring binder to store worksheets in, and write in binder books which are also held in the folder.
Religion: has its own exercise book. sheets glued in as required
English/Bio: for these subjects, each distinct learning area I have a colour coded display folder for. Both worksheets and notes go in these folders. They do, admittently, end up pretty big, but its worked all year, so I don't care.
Remember that you don't have to use one system of organisation for all subjects. For example, I have to do maths in a book, otherwise I would lose the exercises. Other subjects, such as Bio, it would drive me insane if it was done in an exercise book.