With site streams the server only opens a single connection for every 1000 users. Twitter then sends the events of all users over this single connection. The node.js app uses a simple single process message queue to distribute the messages to the actual clients.
If you are running your own streamie server there should be no changes. Site streams are only available to privileged users. If you do not have access, streamie will transparently fall back to user streams. However, the site branch also introduces the usage of a JSON based config file for the server (instead of the ugly command line parameters).