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 App_Data\Templates\BlankSite.
You can find API examples in the following chapters:
Page url: http://devnet.kentico.com/docs/5_5r2/devguide/index.html?sites_api_examples.htm