You can use Kentico CMS API to create new websites or update and delete existing ones. To create a new website, you need to import some of the website templates (typically the Blank website template stored in folder CMSSiteUtils\Templates\BlankSite.
You can find API examples in chapters Import and export of the website, Update website properties and Delete website.
Page url: http://devnet.kentico.com/docs/devguide/index.html?sites_api_examples.htm