It's basically how I keep my journal, but without pictures. Picture is by Eilyn.
I'm currently revising my novel "Crimson Cacophony" [the closest I've come to editing anything longer than 10, 000 words] and I think that if I was a stranger and tried to read the manuscript for the first time, I'd shoot myself with a hunting riffle à la Supernatural. It is a complete mess of a thing and I do mean the actual manuscript, the thing that you read.
Here are the two most important things I'd not to myself and give to you as advice.
1) If you plan on keeping your world-building [especially if that world-building involves, say, a magic system based on the theory that matter vibrates and that it's the frequencies of objects that cause change in the physical world] non-electronically, make sure you use one and the same notebook, journal or whatever for the notes. In my universe, I've gone as far to create a complicated regional and hierarchical society based on talent, skill and the nature of the magic in a person. Magic is way more complicated than that. I involve a bit of linguistics in all of that AND I have no clue where half the stuff I noted down in, so keep all the eggs in one basket. Just this once.
2) If you plan to write the first draft on paper [in my case both my eyes need rest and the story usually flows better, when I write my first drafts by hand, otherwise I keep spotting mistakes in the draft], then make sure you write so that in the end, you can read. Tiniest of the littlest of the beadiest of letters [all swirled into an abbreviation of a word] DO NOT speed up the reading process. Also avoid abbreviations that you are not absolutely sure will make sense to you and never EVER, ever write with light blue pen. If you want to go blind, yes, sure why not, but don't do that to your vision or you will need telescope lenses for your glasses.
Tomorrow I'll blog about what lessons I have learned about writing from reading my first draft and those will be more content related.