If I understand what you're talking about correctly, I do it all the time, separate PHP files for; top navigation, any sidebars that appear on multiple pages, the footer and the breadcrumb if I'm using one.

I code the general layout I want of the site using CSS-styled DIVs and then include all the pages with PHP.

Just so much better, if your nav changes, you change one file, if your footer changes, you change one file, if a site contains 2 or more pages that share common elements then I believe that these common elements should be put in their own file, it just makes everything so much easier.

What problems are you having with the source layout?