I'm not sure I understand backups with Clonezilla. Will Clonezilla erase the destination (backup) disk as it creates a backup or will all the previously saved files be preserved on the backup disk?
Clonezilla can operate in various modes. One of the modes is physical disk to image, which will write an image to a filesystem, without destroying anything present in the filesystem.
Other modes includes device to device, which will destroy the destinations content.