I do something similar with my custom advanced theme. Check the docs on this site for advanced themes, then what you would do is first add these 2 functions:
function header()
{
require_once 'header.php';
parent::header();
}
function footer()
{
parent::footer();
require_once 'footer.php';
}
Then in header.php you just put the HTML from after the <body> tag, right up until where the content will go. In footer.php, everything from just after where the content would end, up until </body>