Include a php file for the whole site

[RonnyK]

I do think that you are overcomplicating the way CMSMS works...

In a pagetemplate you call the logic you want for a page, see the default examples.
In there you call for a DIV#header, f.e. where {sitename}-{title} can be placed to return the sitename of global settings and the pagetitle of the current page..

Putting in {menu} will show the active pages in a menu.
In the content-area, you place {content} and this will place the content as set in the pages at that specific location.

A footer-div, which can call some GlobalContentBlocks f.e. places that text on all pages.

So no direct need for external pages to include in your current setting as far as I see..

Ronny