I track my daily and monthly progress by colouring a square in Excel, and seeing my progress really motivates me to keep it up. I also use the same spread to keep track of my goals and achievements for that month.
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While second drafting, I fill out an index card for every scene in my book. On this card is what characters appear in the scene, what plot (or subplot) the scene belongs to, and a couple other things like if it moves the plot forward and if my character is active. This helps me see the shape of my book, and easily find holes in the plot.
I second draft on paper, and every time I find a problem with plot, character, setting, or pacing (or any other major issue) I write it down in a notebook. Using the index cards I mentioned, I put a sticky note for each problem on the scene that needs changing to fix it. This is based on a method by Susan Dennard, though I’ve changed it a fair bit.
Like most authors, I keep a notebook for each book or series I have. In this notebook I write any random ideas that come to me, keep character notes, but most importantly I use the notebook to second draft and keep track of major changes that need to be made.
I know people who create playlists for each of their books, but I couldn’t live without the visual aid of Pinterest. When an idea is flitting around my head, I spill all those images that keep bugging me onto a Pinterest board. The way I know if I’m really dying to write a story, rather than it just being a temporary shiny idea, is if my Pinterest board has 50+ pins. I know if a story has a hundred pins, I really love the idea, and then I move onto the inception stage of a book where I get to know characters and figure out the world.