We organize by the asset type so it's less confusing. The script, storyboard, and video proof would all have their own folder. For images or supporting assets, we would have one main folder, then have subfolders.
When it comes to multiple versions of a document for a script for example that's a word doc, we version them out. So our folder would look like the below image.
The main folder would contain the latest script, and the subfolder of "Old" would have the past versions.
We also have a naming convention for our documents so the word doc will look something like this: Finance number_Project name_v2.docx
Hope that helps, thanks!