This generally works for me.
General Comics Script Folder
Issue Folder - this and notes are not nested within each other.
Specific Issue Folder
Within these, various things are nested sequentially.
So an issue is
Random I1D1 Breakdown 01
And I do a new draft any time I do significant changes.
For work for hire, I have an extra folder called OPS, with subfolders for each company. This is in the comics scrip folder, but before the project.
I back up to (deep breathe) Drop Box, Carbonite, Gmail, an external hard drive and a thumb drive. And soon Amazon S3.
I believe in paranoia.