For an organizing technique I would use either Google Docs or bubbl.us so the students would be able to ask questions on Google Docs. On bubbl.us, they are able to create their own story lines throughout using the material.
They will be creating stories online so they will use several apps in order to be able to understand what to do, and to think of how to create a story.
For taking notes, they will take the notes, and then send the material to me through a Google Docs
I would create flashcards such as what a main character is, setting, plot, resolution and have the students know the material.
I think it is important that not only should the students take notes, but the notes can be sent to the teacher so the teacher can see if they are on the right track. Its a good way for teachers to double check and see if they hit all the main points
I really like the way you have incorporprated google docs with the students, and used their information to make flash cards. I think it is a great way to get student's input into the classroom environment.