Example of how you can use jQuery to validate 2 email question fields. This example forces an email question with ID 18 to compare with the system email question, if they don't match you can not submit the form.

example.php

<?php // Please do not include the opening PHP tag if you do not already have one

// This adds the JavaScript to the checkout page, it compares an email question (with ID 18) 
// to the system email question and confirms they match.
add_action( 'wp_enqueue_scripts', 'tw_ee_comfirm_email_question_match', 11 );
function tw_ee_comfirm_email_question_match() {
    wp_add_inline_script( 
        'single_page_checkout',
        "jQuery('.ee-reg-form-attendee-dv').each( function() {
            jQuery(this).find('input.ee-reg-qstn-18').attr('equalTo', '#' + jQuery(this).find('input.ee-reg-qstn-email').attr('id'));
        });"
    );
}