Anybody who's remotely paying attention should know that I love Scrivener. I'm near evangelical about its virtues for everything from novel-writing to blog-touring to academic blah organizing. (Yes, my academic blahs need to be organized.)
But there's something that happens to me when I write in Scrivener. It's so easy to start a new file that I end up with a file for every little bit of half-way coherent prose (I'm talking new files for single sentences, folks). Things get so fragmented that I feel like I need a vacuum cleaner to gather it all together again.
What I actually did was to resort to old-fashioned paper, as I explained here. Below are just a few of the zillions of little bits that I needed to place or discard, which was somehow too complicated on the screen. I kept shifting around stuff I really just needed to trash.

The paper solution is working out okay to get me through the end of a draft for novel #3, but I'm thinking... there must be a better way. Not a better way than Scrivener (impossible!), but a better way to use·Scrivener for novel work.·
The problem is that I write stuff before I have a clear sense of organization, not just of the novel itself but even of my writing of the novel. Perhaps the key is to start with better folders for slotting files I'm not ready to use in the MS yet.
I think my problem is that I put too much starter material into Scrivener when I should limit myself to just what is going into the MS. Part of this I blame on Scrivener's awesomeness, which includes handy places to append PDF and image files. That seemed very cool when I had hardly written anything and was hiding behind my research, but now that the MS itself has hundreds of files, those extra sixty down in research are just making me feel all the more encumbered.
For more ideas on how to handle planning and writing in Scrivener, check out this great post, which floats the idea of doing planning in Evernote and reserving Scrivener for "actual" writing.
I may try that for novel #4.
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I do, however, use Evernote for story ideas. Evernote is always open on my desktop and if I am brushing my teeth or working on freelance stuff & have an idea like 'Yes, Amanda needs to get paper cuts!' I just put it in a note for that story. It's much better than writing it down in my paper notebook and then not being able to find it. When it comes time to start or revise that story, I go to the file and all of my random thoughts and inspirations are in one place. I could put them in Scrivener, but opening Scrivener seems so formal, like declaring "I'm ready to write."
The advantage of keeping a thought gathering project like this in Scrivener, instead of Evernote (or something similar), is that you can use Scrivener's organisational tools to keep track of them, and even do a little development on the idea in the thought project. A folder with some cards in it might represent your idea. When it gets to that point where it looks like the idea is starting to spread its wings, you can simply create a new project file, and then drag and drop those items from the thought project into the new project. All of the organisation, keywords, document notes, reference links and so on will carry over to the new project.
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