Don't worry about order, or anything else at that point - just write. Write down character names, relationships to others, attributes, segments of dialog, general narrative, story lines, anything keeping you awake thinking about it. A small desk lamp is helpful if you have an S.O. you don't want to bother with overhead or back lights.
When you have the story well-developed - just type it in free-form without concern for editing. At some point, print the entire thing out, 3-hole punch it, and use bookrings to hold it together so you can flip the pages around easily. Use various colored highlighters and pens and make a key as to what each one means (for speed - green means delete, red - revise, blue - move, etc.) Use letter codes for moving (Move to "A" on page X) and put an "A" with an arrow on page X with an arrow to the insertion point.
Revise, revise, revise - and that mostly means deleting unnecessary shit. You'll be surprised by how much you can get into the story if it has been in your mind for a long time. Use the word count feature to track your progress. Bare minimum if you're going for an agent is about 50K words. There's also Kindle to consider. Just be sure to get at least one person to proof read it at least twice (once to catch your really stupid mistakes and a second time after you've fixed them).
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