If you are running a single schema, technically both parts will be done. However in a split schema environment, the IUA will not upgrade the DATA schema, the upgrade process will require that you run the script to upgrade the DATA schema. That is how it currently works and I'm not aware of plans to change this.
I just realized my responses were not exactly accurate (depending on the version in use and how exactly you're upgrading), so let me correct myself. If you are upgrading to a split schema configuration from a single schema configuration, you cannot only use the GUI. However, if you are doing an IN PLACE upgrade (that is, upgrading the existing schemas that are already in use) of a split schema configuration, the GUI can upgrade both the rules and the data schemas. This is not recommended, but you can choose to do it if you wish. The downside of this, at least in part, is that you cannot continue using the application while the upgrade occurs.