1. Work with both a writer's notebook (for ideas, jottings, images, and freewrites) as well as a computer. Some writers I interviewed used the computer for initial ideas, but many used a notebook. The notebook kept them from over-editing in the early stages. Tips: Number and date your notebooks. Plan time to transfer longhand writing into the computer (one writer started each writing session with 10-15 minutes of this; she said it got her motor going).
2. In early drafts especially, work with a software that helps keep track of versions. Scrivener was hands-down the favorite recommendation. It's cheap ($45) and very intuitive. You can create chapters-to-be as placeholders with ideas listed on the sidebar memo, play with character and place images to inspire you, add research in a split screen, rearrange your chapters' order in a click, and so much more. Buying Scrivener was the best organization decision I ever made.
3. Work in islands, not outlines. I teach the "island" method of developing a book, promoted by writer and teacher Ken Atchity. Basically, you keep a list of possible scene or section topics in your notebook, update it every writing session with a few more ideas, and choose one at random to write about that day. Write anywhere in the book. Great for the right brain, as well as the linear left.
4. Organize your islands by key words. Title each island or scene or section and save it in Scrivener or Word. "Clare--New York museum" "Big flood" "Jonathan--Finding the gold necklace" Key words help you search and locate the scene as your manuscript grows--and helps you avoid duplicating.
Regularly print a list of your islands, a directory of your file folders, or the binder contents in Scrivener, so you can keep track of what you have.
5. Use an image board. Sue Monk Kidd began The Secret Life of Bees with a single image that grew to a board full. I start an image board when I begin a new book. Take an hour and from 2-3 magazines, tear images that appeal to you--no need to wonder why. Arrange and glue them onto a poster or foamcore board and hang in your writing space. Use an image each time you need a freewrite prompt--write about what it means to you. You may find these inform your story much more than you could imagine!
6. Start a dictionary of words you use a lot. Even if you have a manuscript in process, start one now. Do a global search to find your favorites. Mine are deep, twisted, and sparkling--and I use them way too often, as I discovered when my dictionary began to build. Vary your prose.
7. I know I'm going against the digital revolution when I suggest this: Print each complete (bad to great) draft and put it into a binder. Label the binders. Store them where you can find them. Most editors know that it's impossible to really see a manuscript only on the computer screen. Hard copy rocks. Print single-spaced, narrow margins, on scrap paper--most writers have tons of that--to save paper. When your book is published, get rid of them.
8. Use different colored file folders for: (1) unused chapter ideas, (2) research notes and photocopies of research sources, (3) blog posts--if your book is based on your blog, as many are, (4) feedback and critiques.
9. Keep a log of submissions and rejections. An experienced writing buddy helped me create my first log when I began submitting short stories many years ago. Simple, it had five columns: title of piece, date sent, sent to (editor's contact info), sent via (email or snail mail) and answer received. At first, this was all I needed. When I began publishing, I added a sixth column: date of publication. And eventually a seventh: payment received.
10. Many writers use Evernote to gather info from the web, store ideas, and cut down on paper. I love it too, but I still need to physically handle my notes, see my handwriting or typing, read off screen. But do check out Evernote if you haven't heard of it--very worthwhile.