@talisker Backing up your configuration and storage are simply a matter of copying the entire directory in which the config, logs and storage (and possibly others) are kept. If you look at the container's volume configuration, this would be the directory mapped to /var/reactor within the container. Any method of copying will do, including GUI copy to another folder.
Since I don't have a QNAP NAS, I can't advise on how to update the container. Perhaps a QNAP user can chime in on this with some definitive steps. This previous post covered one approach to the process. I don't know if that's the only way, or the best if there are more ways than this one. Please carry on any QNAP-specific upgrade discussion in that (linked) thread.