The second stage of writing a novel, for me, involves collating everything I've learned in the first stage of basic plotting / research, and pinning it all down in terms of where everything should appear in the novel itself. This process is much like story-boarding a movie, but involves nothing more than my writing pad, a pen, and a LOT of thinking.
Before I was signed to a publisher ( and even afterward ) I used to feel a bit guilty for taking a long walk to think about scenes, chapters, characters, pace and dialogue. Especially in the summer. It always used to nag at me that I should be sitting behind my desk, slaving over a hot keyboard and actually writing something. However, I've come to learn that thinking is one of the biggest points about writing: you can't often write a scene without thinking about it first, and writing blind from a blank page often involves copious redrafts, which require thought themselves, which all could have been avoided with a bit of planning and, well, thinking.
So I walk, even if it's just pacing up and down in my office. I often listen to music, picking out movie soundtracks that match in tone the story I am writing as I find this helps visualise scenes much more dynamically. Not only that, but I visualise those scenes as though I'm watching a movie: the dynamics of film often provide a very useful starting point for both scene and dialogue as they're by default very brief and concise: if they weren't films would run for many hours, not two. Then, I jot down notes, piecing major scenes together, getting a feel for mood and pace with each one.
Once I've got enough major scenes ready ( usually between six and ten ) I know I'm ready to start doing my "Story Line". This, for me, is the ABC of writing a novel. I start by taking a clean sheet of A4 paper, and marking a line from top to bottom to make a left margin. At neatly seperated places down that margin, I write the words "Hook, TP1, PONR, TP2, Climax". This is the classic three act structure used by both movies and books. The hook is the first scene ( or even line ) that draws the reader in. TP1 stands for "Turning Point 1", the inciting incident that sets the hero of the story off on their journey. PONR means "Point of No Return": the hero is committed to their cause, often with all bridges of return burned. TP2 is "Turning Point 2", the point in the story where the hero starts to fight back against his or hers antagonists. The Climax, obviously, is the final scenes of the story.
Using this basic plan, I then "peg" the major scenes into place on the storyline, often moving them about, referring to my notes to see if events are occuring logically and if I can see that the story has pace and energy. Between the major scenes I start adding smaller scenes, introducing secondary characters, backstory, and in the case of the Ethan Warner series, revelations both scientific and paranormal that enhance the narrative with interesting bits of real-world research.
After a week or two of tinkering, I have my basic layout before me and I know that it can be written well as a 100,000 word novel. But despite this, I'm not yet ready to open Word and start typing. The next stage of the story involves making my Chapter Map, writing character descriptions for each of the novel's main players, and writing the synopsis for my agent and editor...