Scrivener from Literature and Latte is an amazing writing tool. You can write your novel from scratch within its world of index cards, character sketches, notepads, research, and references, you name it.
I actually find it a little too amazing. I tend to keep track of my characters here, but write my first draft in Word. When the first draft is done, I started revising and putting it into Scrivener where I sort out chapters, add notes, and anything else that needs doing to turn it into a decent manuscript. Once the revisions are complete, I format it into one whole manuscript that I send to my publisher.
I have the app on my Ipad as well and once I worked out the syncing process, found that to be pretty darn handy too.
My biggest tip with starting out on Scrivener is to go through the tutorials first. There are plenty there and they're easy to follow. If you have any issues, there helpdesk people are friendly and, well, helpful.
I've put a quick video tutorial from L&L below. Just click on the big black S above to go to the Literature and Latte website.