One of my goals for this years Nano is to try out Scrivener and if I like it buy it. It is a lot like yWriter but not free. For the money you get a much more polished program. It does have its ways of doing things but it is flexible so you have to work with it to mold it to your style. Here is what I found works for me.
At the left is the binder with folder per chapter and sub documants for each scene in that chapter. To the right is the edit area which I split in two vertically. The left panel is for writing the story's text. It has the complete manuscript so I can go to whatever scene I want. Ilock this so if I click on some scene the text moves to that area but still shows the entire text of the novel. The right split is in outline mode and it shows the index card outline text associated with each scene. You can also expand or collapse each chapter to show the scene details of the chapter summary. This is locked too.
The one downside is that if you put research, characters in a top level section in the binder you can't get to it easily since the panels are locked to the draft manuscript. In NaNo I haven't found that to be a problem. Try it you might like it.