I give long pieces, like novels, their own notebook stack and then break it down like this:
- Chapters. I keep the chapters I'm likely to be working on synced up with Evernote. It's easy enough to do, but how you do it will depend on what writing app you use. You can copy and paste, export your chapters to a text file to load into Evernote, and sometimes even sync directly.
Do you use Evernote? I wish you would. No, I'm not a tout for the company. However, I do feel for the writers who contact me to tell me that their computer died on the same day they bought a USB stick...
I hear tales of woe far too often. You forget to back up, or your backup fails -- they do fail (don't ask) -- Evernote has saved my bacon more than once.
I have several backups, but I still email copies of my works in progress to my Evernote account. It take seconds. Starting a book over again takes way longer than that.