As stated before there is no "automatic upgrade" facility for new versions of ownCloudor for "plug-in/optional" third party software components. An administration "update" feature is available, but will only work on a LAMP server using ownCloud install defaults. Once the "one click install" Amahi package has been updated to a new version of ownCloud the package will have to be reinstalled.
When reinstalling the ownCloud package make sure all data is backed up. To upgrade to the next version of ownCloud instance, replace the files (copy) with the new set from the download. Leave the "config/" directory intact to preserve your ownCloud configuration data. The upgrade will happen automatically upon the next user login.