Backing up app data from two different devices to the same iCloud account
The backup will be overwritten.  

Your Apple ID is what's used to sync data between devices.  It will take the most-recent change as what should be backed-up.  iCloud will think that you want the most-recent change to be shared across devices and it will populate that change to all devices with that same Apple ID.

The way around this would be to use Dropbox or something similar as the backup.  That way you can specify separate folders for the backup and prevent one from overwriting the other.