Nothing will appear in the web pages unless you specifically include it in the html code; that's all the web browser sees.
One approach is to have everything "printed out" by the backend (eg. PHP) code; however that's not really suitable for what you want.
Another is to use a template system such as Smarty. That totally separates the backend code from the visual appearance of the site.
With that, a PHP backend purely generates the data that varies from page to page, and feeds that to the template engine. When everything is ready, it tells the engine to use a specific template file to display that page.
The templates are just html pages [with a different suffix], with inserts where you want the changeable data to appear.
It's a perfect split between backend and display [html] code.
It can also do things like looping, so for eg. a variable size table or list, you can pass the number of entries and an array of data, then the template automatically show the correct number of data rows or sections
It also caches the templates as it compiles them so after the first view of a page (new or after editing) it does not slow the site down - and can actually improve responses.
http://www.smarty.net/
It needs a bit of setting up on the web server, but it's quite straightforward and well documented.