Yes, you should use FastCGI mode and let nginx/Apache/whatever deal with being the webserver. HHVM's old built-in webserver has been deprecated for quite a number of releases now -- I can't find the old the wiki page on its deprecation, but it's been about six months or so. This more closely mirrors how PHP is often used, and removes a whole host of complicated HHVM-specific configuration mess. Many people are already familiar with how to make nginx/Apache serve files the way they want, and so we can just keep the HHVM-specific stuff in HHVM and let the full-featured webservers do what they are good at.
The getting started guide has a very quick, basic intro to getting FastCGI set up if you're using our prebuilt debian/ubuntu packages, and the FastCGI wiki page contains all the details to get set up in some other environment.