What does Page Content contain in Panels Everywhere when site template is enabled?
A page panel will be placed where the main page content is located.  The page panel will be displayed only when the conditions of its Selection rules and Contexts are satisfied.  You can define alternatives by creating multiple variants for the panel and modifying the settings to meet your needs.  Panels will search through the variants and go with the first variant that meets the criteria so the order you place the variants in may matter.  Using Panels Everywhere, you would set the overall layout for your site pages in variants to the default site panel.  The various page panels would then be displayed in the regions as defined for them.  

You can also create mini-panels and view content panes which act similar to blocks except that, like page panels, you can define selection rules and contexts for them and place them anywhere else on the default panel variants you desire.  So you can provide content related to your main content based upon the context (users, tax terms, field settings etc.) that apply to the main content display.

I'm not sure if I've fully answered your question.  What do you want to achieve in your site setup?