Everyone Needs Their Own Method
Throughout the years, I found my greatest challenge to be the discovery of an organizational system that worked for me. All of you who are still struggling with that first novel need to overcome that challenge.
I tried postcards pinned to the wall, until I became embarrassed by the number of trees I was destroying. I tried Dragon Speaking so that I could dictate the book, but it took forever to train the application. And, I tried a half dozen other methods.
In the end, with my many years spent in the corporate world, I chose MS Office 2010, which gave me the control I needed. Using an outline format, with the side navigator bar allowing me to jump and search, I was able to cut, move, and edit the plot until I was ready to write.
Then, it was just a matter of developing my outline, many areas containing dialog, into my first draft.