_site/ will be deleted. You are not supposed to create anything inside
_site/, you create outside (in your project’s root directory). When jekyll builds your site, jekyll will create a new
_site/ folder with your site.
You can take a look at the documentation on how to structure your files.
You just create your stuff in the root folder (of your project), and not inside
_site/. It is hard to tell you where exactly to put your stuff because it is not clear what is your site structured. If you provide more information about it, it will be easier. E.g.: have you created your site following the Quick-start guide or have you cloned a project? (: