I've used notebooks for decades. I buy a kind that is pre-numbered, and in which the pages larger than 8.5x11 inches, so I can tape in graphs and printouts of US letter size.

During my PhD, when I was scared of losing things, I made photocopies of my books when I completed them, and kept the copies in a separate location ... now I can scan them.

I have a simple cross-reference scheme. To refer to a result on page N of book M, I write [M.N]. If it's a certain figure or equation on that page, I just write e.g. [M.N.f3] or [N.M.e5].

So far, I think this is all quite conventional. But I do one more thing that's simple but has proved to be very helpful. I write forward references in the top margin of pages. So, if book 10 page 3 refers to book 2 page 9, I write <10.3> in the top margin of page [2.9]. This simple scheme makes it really easy to take care of ripple effects of errors.

Oh, and you've got to use pen, and you've got to use clean cross-outs when you find errors. Otherwise you'll get hopelessly lost.