I can recommend this drawing for the initial and generic understanding of Lync protocol work flows.
Think for example about the Mediation Server, you have Media Bypass, Early Media and other related configuration, which are all not reflected and will therefore genrate a huge impact on network design, or Firewall setup's in Enterprise Networks. It also do not show the Mediation Server <-> Gateway connect.
Download here: http://www.microsoft.com/en-us/download/details.aspx?id=6797
Author: Thomas Pött Managing Consultant Microsoft UC