As earlier mentioned in the FAQ, you can run NodeJS app either in developer mode or in production mode. Refer to this link for more details w.r.t. that.
Now lets say you are running your app as /app1 , the various static assets like images, css, js etc., should be placed under the VHost's/Website's folder i.e. /home/{username}/{vhost}_public_html/app1 .
If you were running your app as / or as website root, then all assets should be placed under /home/{username}/vhost_public_html