I've got a website that as about 6000 hits a month so don't want to hurt it in any way, but I want to make the header and footer into php files but not turn the rest of the page php, because I don't want to lose all the links to them, will that be seen as bad code by the search engines?
You should research how to create .htaccess file. You can use old url with .htaccess and have footer and header with php codes.
Search engines cannot see any PHP coding, so Google (for example) won't know if you're using a header.php file or a footer.php file. Search engines only see the final output of a website. As was said above, use a .htaccess file to treat your .HTML files as .PHP (whilst still keeping the .HTML extension). A quick search would bring up how to do this.
The module is rewrite_mod and the process is called URL Rewriting. It's a bit involved and tricky task. Maybe you'll need to hire someone to do it. I would recommend using a MySQL table to store what must be served when what is asked. Here is the code I used in a project I built: This goes into .htacess: RewriteEngine on RewriteRule !(^.{0,}\.[a-zA-Z0-9\.]{1,4}$|^$) url_router.php Code (markup): And this goes into the url router: <?php require_once("init.php"); if(isset($_GET['no_route'])) { $url_router_file=$_SERVER['DOCUMENT_ROOT'].$_SERVER['REQUEST_URI']; $url_router_file=strstr($url_router_file,"?",true); include("mime_type.php"); header("Content-type: ".get_mime_type(pathinfo($url_router_file,PATHINFO_EXTENSION))); readfile($url_router_file); exit(); } $url_router_uri = str_replace(BASE_URL_RELATIVE,'',$_SERVER['REQUEST_URI']); if(strpos($url_router_uri,"?"))$url_router_uri=strstr($url_router_uri,"?",true); $url_router_hooks=array(); execute_action("pretty_link",array(&$url_router_hooks));//array of array("pattern","file_to_be_executed") $url_router_hook=""; foreach($url_router_hooks as $hook) { if(preg_match($hook[0],$url_router_uri)) { $url_router_hook=$hook[1]; break; } } if($url_router_hook!="") include($url_router_hook); else { include("errors.php"); } ?> Code (markup): As you might see, the php code has loads of dependencies which are defined in the init.php of my project. I won't be able to post it here as the project is not open source. If you want me to help you with it for a fee, PM or mail at technofreak777[at]gmail.com
I totally agreed with you.The search engine actually see final output of the site. Even if you code server side scripting , the final output of html or php file actually dooes matter for search engine.