The great thing about organizing your writing, is that there is no one right way to do it. The best way to do it, is whatever works for you. This often comes down to personal preference and style. Different writers also want/need different levels of organization, running the whole gambit of micromanaging to only placing the biggest "landmarks" of a story to hit along the way.
My presentation to the students focused on giving a few ideas to try out to see what works for them. I encouraged them to organize both their plot, but also their characters.
Here are some of the ideas:
Organizing Your Plot:
o Sticky notes: Write down scenes or events that will happen and then rearrange them. (Put them in the beginning, middle and end piles)
Organizing Your Characters:
See the entire presentation here, and find out how writing a good plot is liking riding a good roller coaster. (The presentation is attached to the page and is called "Organizing Your Writing.pptx")
Feel free to post additional idea you have!