using php includes in the templagte should not be a problem as long as you add the includes to the template outside of the editable regions.
If you add the includes inside the editable region, they will not be applied to the pages based on the template.
same thing for changes made to the child pages, the only changes that are applied from the template to the child pages are changes made outside of the editable regions.
when you edit the template, content outside of editable regions is applied to the child pages.
on the child pages, the content inside the editable regions is not touched.