One can never have too much advice, I suppose.
I did a lot of searching, reading, and researching the various methods for organizing a novel, and what I've done here is to take bits and pieces of advice given by other authors, writers, editors, etc. and meld them all in to a process that worked best for me. This doesn't mean that this is going to be what works for you, but I found this to be the easiest and most comfortable method for working on my novel that didn't end up feeling like "busy work."
If you've made it this far in the process to the point where you're figuring how to organize your plot, you've probably already got some kind of a.) a character, or b.) an idea for your book. If you don't, don't worry! We'll figure that out, too. No matter how simple or vague your idea, this plotting method is going to help lay things out in a way so that other great ideas are going to be fighting tooth and nail to make it onto your big list o' plot. Keep a pen at the ready, and stay alert.
I began this process with a 2,600-word opening-scene (actually, two opening scenes) draft that I'd started during last year's NaNoWriMo, before I apparently got abducted by aliens or whatever happened that made me throw in the towel just a few days into the month, but you can begin yours however you'd like. Blank sheet of paper? No big deal. Half-finished manuscript? That works, too. Whatever you've got, bring it to the table and let's get ready to novel.
Writing it Out.
At this point, don't even worry about using your index cards, unless you're hot and want to splay them open like a fan. This part of the process is going to go a lot quicker and in a much more orderly fashion if you have everything laid out on one page so you can see where you've come from and where you may be heading. Those index cards will have their moment of glory, but first, a little work.
Open a Word document (or grab a pen and a blank sheet of paper) and type or write the number one. It should look like this: 1. Now write a brief sentence (or two or three) summarizing your first scene. Hit enter. Write the number 2. Write another brief sentence summarizing your second scene. Hit enter.
The goal here is to shoot for roughly sixty scenes. (If each scene in your novel averages 1,200 words, you're looking at 72,000 words when all is said and done. It's still a little on the short side, but it's a great start, and more than what is required to successfully complete NaNoWriMo. If your scenes are in the 1,500-word range, congratulations - your completed manuscript will weigh in at roughly 90,000 words. Pretty respectable, chum, so give yourself a pat on the back.)
Think in terms of television, something we are all used to these days. We like action. We want the scenes to change. We want to get lost in camera angles. If you're striving for a longer work, add more scenes rather than extending the scenes too long, unless your goal/idea/masterpiece/experiment involves a novel that reads more like a series of short stories than chapters. Anything longer and the story may start to lose its pace.
(Of course, there are exceptions to every rule. This is your novel, so you write what works for you.)
At this point, some writers suggest splitting the scenes up evenly between characters, so if you're shooting for 60 scenes, give 20 to your main character, 20 to the villain, 10 to side character A, and 10 to side character B. I don't agree with this method, so I don't follow it. To me, it seems contrived. I'd rather let the story flow out on its own without trying to assign characters right now. Later, if I see that side character B is only featured twice, maybe I'll consider getting rid of him or her, or morphing him or her into side character A, but that's later.
Back in your Word document or handy dandy notebook paper, continue listing scenes you'd like to appear in your work. It doesn't matter if they stay in order. If you are struck with a brilliant idea for the end of the story but you're only on number six, go ahead and write it now, giving your future self some sort of clue that it happens later. Like this:
6. Later, Stacey is going to find the missing aardvark. It will have Larry's burrito tied around its tail. I think she's going to be mad, and might end up shooting him -- Larry, that is. Or maybe the aardvark. Or maybe both.
At this point, things don't need to be too detailed. Of course, if you have an awesome idea that involves details, type them in, too, (or write them in, if you're penciling or penning) so you don't forget them later. The point is to just keep going to see what you can come up with. If you like fight scenes, try one out! Throw it in. What kinds of situations would you like to see your characters in? If it resonates with you, you're going to believe it. If you believe it, and you write it like you believe it, your readers are going to believe it.
Don't be afraid to be mean to your characters. Throw something on the page and see if it sticks. Odds are, one small idea will lead to an idea for another scene, and then another, and then another. Keep going until you reach what you consider the end.
The More You Know: Character
The more you build your plot, the stronger you're going to get some sense of your characters. If you add a skinny-dipping scene and your main character is in the back of your mind, screaming, "Yes! Yes! Yes!" like a college frat boy, odds are you've just learned something about him. Jot it down on a character sheet. I prefer a plain piece of paper (or new Word document) for character. Nothing fancy, just some ideas. Other writers/authors suggest doing a "character interview," or filling out a character sheet that involves everything from their favorite television show to when they stopped wetting the bed, but I don't think those are necessary right now. They may come in handy down the road, however, if you're writing from a certain character's point of view. Capturing the voice of the character will be easier if you know how well-read they are, for example, or what they do for a living. Or their political view.
No one wants to read a novel about Jim, the sheep salesman, who goes around one day, sells a bunch of sheep, and goes home. Nothing happens that we don't already know based on Jim's job. In order for the reader to stay interested, we need to see Jim get hit with some sick and twisted shit, and that's the truth.
Jim goes next door to sell a sheep. His neighbor answers the door wearing nothing but cotton, only I'm talking cotton balls. And she only uses three of them. Jim, usually a pretty shy and vanilla guy, has just seen his ultimate fantasy come true. What does he do? Run away? Loosen his tie and head inside? Call the police and report his neighbor's strange behavior? You decide. But whatever it is that Jim does, it better say something about Jim, even if he tries something out of the ordinary. If Jim would normally be a "turn tail and run" guy but decides, in this situation, to stick it out and see where it goes, we need to know that. Show us that Jim is nervous, that this is new to him. Does he start to sweat? Does he need a glass of water? Does he ask for one repeatedly, his voice cracking? You get the picture.
On Jim's character page, write down how doing something "out of the norm" makes him feel. Strong? Brave? Heroic? Nervous? Nauseous? Uncomfortable? Note it, and move on.
Oh no. Maybe, like me, you've only made it to 24 scenes and your story just wrapped itself up. The neat little package is beautiful. All loose ends have been resolved, someone died, someone lived, and the world is the way it's supposed to be. You've got a handful of characters, a great story line, some intense high spots/low spots/action scenes, but you've only made it to the number 24. What now?
Once you feel finished, print. Hell, even if you only feel 80% finished, print. This isn't the final draft, for crying out loud. Make sure your scene pages are double-spaced (at least) with plenty of room in the margins. Five minutes after you print this, you want to make sure you have plenty of room to write those great ideas that are going to continue rolling in. That's okay. Slide them in where you can. Write on the back. Make an elaborate asterisk code. Use stars, exclamation points, whatever you need to do. Just jot. When you eventually need to retype, that's fine too, but shoot for just jotting for now.
Now print out (or write out) the character sheets for each of your main characters. These don't need to be numbered or bulleted, and probably don't even need to be double-spaced: you can just jot on the bottom of the sheet if additional inspiration strikes, and/or cross out if necessary.
If you find you've only made it to number 24 on your plot/scene page, there are a few options, because I know you love options. You can add more scenes, add more characters, or try starting the exercise again using a side story. Don't freak. This may be something larger than or "outside" your characters. Government shutdown? Hostile corporate takeover? The greenhouse effect? Either way, shoot for ideas that can work as a side theme or side story. Maybe it will end up entwined within your main story somehow. Odds are, if you're still inspired and still coming up with ideas, it will fit.
If that doesn't seem to work for you, don't sweat it. If you build it, they will come, or so Kevin Costner said. Just start with what you've got and go from there. There are no concrete rules for your novel, so you do what works best for you.
Finally, the index cards.Your scenes are written. Your novel is complete. You've done it. Everything worked out exactly how you wanted, and they all lived happily ever after, or they didn't. Once everything is said and done, now it's time to shuffle.
Remember your scene sentence summary - the exercise where you initially only made it to 24? Think about how it compares with the finished product. On an index card, write a one sentence summary for each scene that made it into the final cut. Number them, so you can revert back to their original order if necessary. Lay them out in that order.
Once you have them laid out, take your hands and mess them all up. Probably a better idea is to move a few chunks around, a little at a time. Does a different order change the story? Is it better to start closer to the action, telling the "beginning parts" as back story? Experiment. Get crazy. What if you start with the last scene? What if you worked backward? Sorry, maybe that's a bit too risque, but I think a lot can happen when you change the order around.
Whatever order you decide on and however your novel turns out, keep those index cards. Once you submit your manuscript to an agent or publisher, they might make a recommendation that has to do with the timeline. Typically, your story needs to start with a hook - something to keep the reader invested in the story and characters. If you don't have that within the first few pages, your story may never make it to print. If you can't keep a slush reader interested, your manuscript gets used for kindling. If the action takes place when the character turns 25 years of age but you needed to include a story from his childhood because it's pertinent to the plot, for Pete's sake do not start the novel chronologically.
Make sense? Good.
That's my interpretation of the whole index card thing. Maybe it's less "index card," more "scene development." You be the judge. Just remember, at the end of the day, do what works for you. If you tried my method and hated it, Google another method, or (probably a better idea) do what comes naturally to you. There is a story inside you, waiting to be written. Get it on paper first, and the polishing, cleaning, and organizing can come later.