You can do manual backups by tapping Options in the library and then tapping Backup All. Please make sure the backup file is transferred to your computer for safety.
If you use cloud storage such as Dropbox, GoodNotes can upload your documents automatically to the cloud storage. It can be enabled from Options > Settings > Automatic Backup.
Warning: if a file failed to upload, GoodNotes does not attempt to re-upload in the current version. Large files may take too much time to upload than the allowed time for apps to remain in background and become missing as a result. We plan to fix it in future versions.
Backing Up Documents in iCloud:
If you are using iCloud sync with GoodNotes, please note that iCloud/iTunes backups do not include your documents in iCloud. You can use the manual backup method above, or if you have a Mac logged into the same iCloud account, you can use Time Machine to backup your iCloud data.
Backing Up Documents Stored Locally:
If you are not using iCloud sync with GoodNotes, your documents are stored locally on your device. Both iCloud and iTunes backup will include your GoodNotes documents. More details about iCloud/iTunes backup can be found here.