You're right, good file organization skills are very important!
The good thing about an iMovie project is that it saves a copy of the media files within itself.
To see the media files within an iMovie project:
1. CTRL-Click on the file in the Finder.
2. Choose "View Package Contents"
3. Navigate to the Media folder.
- Don't move any items within the package as this may mess up your iMovie project...
It might help to organize your media by using a folder and naming convention system e.g.
That would be an example of creating an easy to find system with associated folder to keep assets in.
Also, although backing up to external HD is extremely good practice, remember that HD's can fail and you may even overwrite some important data by mistake.
For really important files keep a second back up. Some would recommend using dead media (DVD/CD) for each project as opposed to an HD.
This is the question you're asking, right?