Put everything into WordPress. This way, you can search your entire content from the built-in search engine, and you can edit each piece.
If you need pages with special markup create templates for your theme.
Naked Template
<?php
/*
* Template Name: Naked
*
* That’s the complete template!
*/
Basic HTML5
<?php
/*
* Template Name: Basic HTML5
*/
?>
<!doctype html>
<meta charset="<?php bloginfo( 'charset' ); ?>">
<title><?php wp_title( '' ); ?></title>
<?php
while ( have_posts() )
{
the_post();
?>
<h1><a href="<?php the_permalink(); ?>"><?php the_title(); ?></a></h1>
<?php
the_content();
}