1. Create Your Roadmap
If you did not create your first draft from an outline, now is the time. Your outline is a roadmap that will keep you on the right track as you move through the book. This is particularly important for mysteries and thrillers, which tend to have plots that are complicated enough to confuse even the author.
Write an outline of the entire book, chapter by chapter, as it is currently written (even if you intend to change everything.) You should be able to summarize each chapter in a single sentence or bullet point. You should also be able to detail each chapter in a single paragraph. If you're unable to do this for some of your chapters, you might have too much going on in those chapters. In a novel, there is plenty of time for each subplot to develop, so don't throw too much at the reader at one time, leaving him/her confused. You also don't want to give away too much at the beginning. Let themes have time to develop.
2. Plot Your Plots
If your outline above looks more like a mangled spider web than a roadmap, you might need to take a step back. Make a list of your subplots. Summarize each subplot as its own little mini-story in three paragraphs or less. There should not be more than about four or five main subplots in a novel. Most novels in the mystery and thriller genres have two or three.
Now go back to your outline. Flag places in the story where each subplot can be introduced and developed. Also flag places where subplots share a common theme. These are the places where they can potentially be woven together. A common pitfall of newer or less experienced authors is to create different subplots that never quite mesh. Make sure from the beginning that your subplots will eventually interweave.
3. Hone Your Acting Skills
Once you have established your subplots and outlined how to develop them, it is time to define and refine your characters. First, make a list of all of your major characters (including historical figures, ghosts, villains whose identity has yet to be discovered, etc.) Find spots in your outline to introduce and develop each of them. Try to introduce all of your major characters in the first third of the book. If you have more than about ten main characters, you might have too many and readers might have trouble keeping track of them. Ask yourself if all of them are necessary or if roles can be merged. On the other hand, if you have fewer than about five major characters, your story might be a bit thin and adding a subplot or two might be in order. Also make a list of minor characters. Decide who needs a name and who can simply be "the concierge" or "the limo driver." Decide if any of these minor characters will come up again.
For each character you decide to keep, make a short list of physical traits and personality traits. Does the character have an accent? A limp? What are his go-to words in dialog? As you develop scenes, keep these character traits consistent. If your character's mood changes halfway through a scene, something has to have triggered that change. If her English is poor in her first scene, she can't develop a sudden eloquence later.
4. Wrap it Up
In summarizing each of your subplots, you should have developed an understanding of how it will end. You also need to decide where each of your characters will be at the end of the novel. If you are writing a mystery or thriller, some of your characters might wind up dead. Others might land in jail, find fame and fortune, or simply return to the mundane life they had before this whole thing began. When planning your first revision, it can be helpful to consider what will happen to each character before the end of the story and how each of their fates can play into the final scenes of the novel.
5. Revise and Repeat
You should now have an outline of your first draft story that is annotated with the places where each subplot and each character will be created, developed and interwoven. You should also have a firm understanding of how the story as a whole will reach a resolution in the end, and what will happen to each of your main characters. Are there "extra" parts in your outline at this point? They might not fit into the story. Consider cutting them now, rather than potentially following a tangent that leads away from your main plots. If you think an unaccounted for piece is just too good to cut, then reconsider the subplots you have established and decide if any of those should be replaced or refined.
Now comes the fun part. Go back to your first draft with your outline beside you and use the cut/paste functions on your computer ad nauseum until you have placed each chunk of your novel where it belongs. Fill in the missing components. Then re-read your whole masterpiece and revise again.
Do you tend to write from an outline, or just wing it?