OK found it.
Follow the link in the Home tab through to your homepage (or blog page). Then find the Page specific Yeost SEO settings. Here use the general tab to set the description.
Edit: You don't even have to get there via the plugin settings. Individual page settings appear on your page editor, so you can update this directly while editing a page. Look for and click on 'SEO - Check'. These settings will show up in different places (alongside page/post content, or below it) depending on your WordPress display settings.