See: What is EZPages? Link for detailed use of EZPages
This Link could show in the Header, Footer or Sidebox or a combination of all three locations.
The Chapter and TOC settings are for using this Page in combination with other Pages.
The other Pages can be shown either *only* with this Link in the Chapter and TOC or as their own Link in the Header, Footer or Sidebox, depending on how you would like them to appear on your site.
There is no true "Master" Link, other than the Links you actually have configured to display. But any Link in a Chapter can be displayed in any of the 3 locations for the Header, Footer or Sidebox or not at all, where it only appears together with the other Links in the Chapter.