For updates within a Fedora release (for example, Fedora 23 Atomic Host), you would use the `atomic host upgrade` or `atomic host deploy` to set up a specific tree from your composed repo. This is the standard mechanism for updating the host OS.
For upgrading to a new Fedora release (for example, from Fedora 23 Atomic Host to Fedora 24), the standard mechanisms don't work. Instead you need to add a new tree repo to sync and re-baseline. The wiki page shows how you would go about doing that, and that uses the `ostree` commands. You could replace the last `rpm-ostree` command with the `atomic host rebase` command, if you wanted to.