Aside from the sync services such as contacts, mail, etc, the only way other data in the form of files are saved to iCloud are 1) a backup of app data to iCloud (this assumes backups are turned on as well as the app, see Settings>iCloud>storage and backups), and 2) individual apps that save their own data files, not as backups per se, but for syncing purposes.
I'm assuming you have been discussing (2). you haven't mentioned doing a restore, and I wouldn't recommend that at this point. Version control if it were used would have to be the responsibility of the app. iCloud does not implement that on its own and I'm sure Apple wouldn't want to provide that feature as users would quickly run out of iCloud storage.