To update files in the ecryptfs filesystem you need to update them in the mount point - in the encrypted filesystem you would need to update the entire thing at once, as it has no concept of files or directories - it is just a large chunk of data.
Yes, you can use rsync to back that data up somewhere, but in order to read or write a particular file you need to mount it.
You can mount it from various different places (probably best not to try this simultaneously :-) so why not use a shell script which mounts, rsync's the relevant files and unmounts whenever relevant files are updated?
useful info here
