How does having to move the project file to Dropbox effect external backups?

I’m trying to figure out how to link my Mac and iPad together through Dropbox. Now, from what I understand it is necessary to move the project file from my computer document folder to the Dropbox folder. Wouldn’t this effect my external backups?

The entire Dropbox is mirrored on your Mac (usually in ~/Dropbox). And that folder would then just go into your backups like any other folder.