deploy and map to a dir that does not have a web path

I am trying to setup a remote server, but my root path for my project is not the root of the website.

my file structure looks like this
/var/www/project  -- root of project (config files live here)
/var/www/project/site  -- htdocs root (ex. www.website.com)
/var/www/project/api   -- htdocs root (ex. api.website.com)

How do I setup a mapping for this because the ide complains if I don't have a mapping for the project root, and I cannot setup a mapping without a project root?