Validation Issues

I tried to submit my question through the HTML Writers Guild but I kept receiving an error page - http://www.qpost.com/ask.
My Question
What is the proper way to code Include files and still validate the content pages where all the code is compiled? My pages for the site validate by file upload method but not URL because of the include files not having DOCTYPE & Heading code. When I added that code to the Include files the pages don't validate because it reads it as having multiple DOCTYPE's & Head tags.
http://www.alvincollege.edu/default.htm