Using twitter bootstrap in a theme

Almost.

Put the bootstrap stuff in your theme, and include it on the front end using wp_enqueue_style and wp_enqueue_script in functions.php

e.g. for the bootstrap js:

function my_scripts_method() {
    wp_enqueue_script(
        'bootstrap-js',
        get_template_directory_uri() . '/js/bootstrap.min.js',
        array('jquery')
    );
}
add_action('wp_enqueue_scripts', 'my_scripts_method');

And for bootstrap.css:

add_action( 'wp_enqueue_scripts', 'prefix_add_my_stylesheet' );
function prefix_add_my_stylesheet() {
    // Respects SSL, Style.css is relative to the current file
    wp_register_style( 'bootstrap-css', get_template_directory_uri() . '/bootstrap.css';
    wp_enqueue_style( 'bootstrap-css' );
}