When writing, editing and re-writing, there are a lot of details within your book that you will either delete, rearrange or hide away for safe keeping. That's right, it's not always as simple as putting your pen to paper (or finger-tips to keyboard) and creating scenes from start to finish. There are many different ways you can make it easier for yourself as a writer, that will also help improve the quality of your story. It all comes down to extra notes.
Editing notes
If you're a part of the writing community you surely would have heard of people with documents upon documents of notes or edits for each book, just so that they don't mess with their original writing attempts. This is definitely something for people to follow along with, as sometimes us writers change our minds. The worst thing you could possibly do is delete a previous idea that you momentarily thought was weak, only to wish you had the same wording available the next day.
Most editing I personally am experienced with can be done through Microsoft Track Changes, and I know that most professional editors make sure to create another document with the Track Changes accepted instead of deleting work from the original. This is because you need to be able to review the changes, and sometimes changes aren't always for the better.
If you don't want to (or don't have the computer space to) create an entire duplicate of your manuscript for changes to be made, then you can always make a small document with your deleted content. These should be copied and pasted straight onto an empty document, with specification of what page and section they came from, in order to save future confusion. By doing this, you can progress your work without worry of losing any prime material from your original manuscript.
Plot and story notes
When writing novels, there are going to be a lot of pages holding information that you may not be able to easily think of later on. Because of this, it's important to plan your work accordingly - with notes in special categories. I'll break some down for you:
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Characters The makings of a good story places a high importance on how dimensional your characters are, and developing characters takes time. A great character can also be ruined by inconsistency, so there is a lot to look out for. But how can we do our best to keep our characters consistent throughout the whole process? Create an entire document or powerpoint dedicated to your characters, before you begin writing. Here, write their names, their relatives, a brief background story and most importantly their motives. Once you have the foundations, it's simply the case of regularly updating their details as your story moves along. Even if you reference something like their street address once - write it in the character notes, so that you don't get it wrong if you can't find it again. When writing a book with a large amount of characters, this will also help you to keep track and not accidentally forget about someone who might've been introduced early on with presumed character potential.
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Foreshadowing As you're aware, great books usually have little hints to the readers on how the story will progress. It's what stops endings from seeming out of place or out of character. However, these are something you also need to keep track of. Like when editing, it's important to keep a note of where you put an example of foreshadowing in your book - including what page number, paragraph, etc. This allows you to elaborate on your hints, and to potentially shift them if the trajectory of your novel's plot changes.
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Dialogue style This is another important one for your character consistency. We learn most about our characters through the way they speak and what they say. Whether its their slang, their accent or their 'on-purpose' quirky way of pronunciation, you want to make sure it doesn't change throughout the novel (unless it's part of their character development, of course). As a popular example, if you write a character to have a thick French accent, replacing 'the' with 'zee' within their quotes, you can't accidentally fall short or give up on the sentiment. If a character has had a French accent their entire lives, it's unlikely that they'd lose it within the short span of your novel's timeline. Therefore, you need to make clear notes - almost as if it were a glossary - about the way words are pronounced, if some words mean something else to the character, and how to maintain their mannerisms throughout the novel. Just a simple reminder to yourself will help to keep your characters realistic.