The update script considers all entries in the schema.yml files. So just enter all custom database modifications into the schema.yml files as well.
If that is the case, the update script considers all modifications automatically, as it gathers its information from these files and compares them with the current database.
Important: It is imperative to update the schema.yml files before the update in order to not overwrite any database modifications. Therefore unpack the tar.gz from the update package, edit the according schema.yml files and start the update task manually afterwards (as described in the UPDATE file).
