The first one allows you to set the API key used to connect to your WP Lookout account:
$ wp wplookout set_api_key <key>
The second one allows you to hide the WP Lookout settings page from the WordPress admin interface:
$ wp wplookout hide_settings_page <true|false>
Using these commands as a part of a site setup or maintenance script allows you to get WP Lookout in use quickly on all of your client sites.
As always, you can also continue using WP Lookout without our plugin and without touching WordPress sites at all; our tracking works independently of how a given site is configured.