Backup files always need to be created on your device first and can only once created be uploaded to the cloud. So if you do not have enough space to create a full backup, you need to create a database only backup and then use iTunes Filesharing to save the contents of the Stage Traxx 3 folder on the iPad to your computer.
To restore it, you first need to copy everything back to the ST3 folder and then you can restore the database only backup.
Regarding the Save button: I haven't heard about this issue yet. What iOS version are you running? Does the button appear if you rotate the screen?