No, Apple's iCloud service does not currently integrate with iAnnotate for automatic backup of your work. iCloud does not preserve the documents stored on your iPad, nor the annotations made to those documents in iAnnotate.
For automatic backup and storage of annotated files, please set up a connection to one of the supported cloud services listed below:
OneDrive (formerly SkyDrive)
If these cloud services are not an option, iTunes file sharing can be used to make manual backups instead.