If you want to add a brand new site into existing instance, please follow the documentation. It says in one of the info boxes:
Installing new MVC sites into existing Kentico instances
If you wish to add the new MVC site into an existing Kentico administration project, set the target location to the given project's installation folder.
In this scenario, the installer adds the MVC project into the specified folder and uses the administration project's existing database. A new Kentico administration project is not created.