Engineering Paper FTW (for the win):

https://www.amazon.com/Tops-Engineering-Computation-Punched-...

I assume most middle school teachers specify how papers should be organized in binders and labeled with names, dates, etc; but below was my method I developed halfway through college:

Top Margin use: left - name, center - class, right - date

One binder per semester; a divider for each class; handouts, tests, etc were hole-punched and placed with my notes in chronological order.

If my notes didn't make sense as I was copying down what the professor did, I would rewrite my notes later that day while figuring the problem-solving process out and making the notes/arithmetic easier to follow.

This method also applied to non-math-related classes.