how to create template path for external (include) .js file

Use wp_enqueue_script(), hooked in via an appropriate action hook callback.

wp_enqueue_script(
    // Script handle
    'someScript',
    // URL
    get_template_directory_uri() . '/js/someScript.js',
    // Dependencies
    array( 'jquery' ),
    // Version
    '2.4',
    // Output in footer?
    false
);

For example:

function wpse72720_enqueue_scripts() {
    if ( ! is_admin() ) {

        wp_enqueue_script(
            'mathUtils',
            get_template_directory_uri() . '/js/mathUtils.js',
            array(),
            '',
            false
        );

        wp_enqueue_script(
            'superfish',
            get_template_directory_uri() . '/js/superfish.js',
            array( 'jquery' ),
            '',
            false
        );

        wp_enqueue_script(
            'switcher',
            get_template_directory_uri() . '/js/switcher.js',
            array(),
            '',
            false
        );

        wp_enqueue_script(
            'query.mousewhel',
            get_template_directory_uri() . '/js/query.mousewhel.js',
            array( 'jquery' ),
            '',
            false
        );
    }
}
add_action( 'wp_enqueue_scripts', 'wpse72720_enqueue_scripts' );