Site content for a given domain or subdomain is served from its document root. (the base folder from which all content is served)
All accounts have a document root for the primary domain under /var/www/html. The Folder mainwebsite_html is a reference/link to it.
When adding a a domain via DNS > Addon Domains or creating a subdomain (Web > Subdomains), then the directory specified will be the location from which content for it is served.