Depends if you want to add your CSS or JS conditionnaly. If you want them to be included in all files, just use the functions.php page of your theme folder, and add :
function your_scripts() {
wp_register_script('yourscriptname', '/PATH/TO/YOUR/SCRIPT.js', false);
// This registers your script with a name so you can call it to enqueue it
wp_enqueue_script( 'yourscriptname' );
// enqueuing your script ensures it will be inserted in the propoer place in the header section
}
add_action('wp_enqueue_scripts', 'your_scripts');
// This hook executes the enqueuing of your script at the proper moment.
For the stylesheet, proceed this way :
function your_css() {
wp_register_style( 'nameofyourCSSsheet', '/PATH/TO/YOUR/STYLESHEET.css' );
wp_enqueue_style( 'nameofyourCSSsheet' );
}
add_action( 'wp_enqueue_scripts', 'your_css' );
// same hook is used to enqueue CSS sheets
header.phpas you'd normally do with a static html page.