That's some useful information. I tend to just wing most stories and hope they come together. My longer works I like to write chapter titles and then shuffle them up and put them into a logical order.

After that, I flesh out the scenes with the same number of items as I hope to make pages (so I have 1 scene snippet per page). Then all I have to do is fill-in-the-blanks, basically.

On a side note for tools, I use Trello everyday for work, it's a nice way to chunk the workload into manageable pieces. It's great for Programmers as it's just like using functions, so it's something my mind can wrap itself around.