A simple example of how to set all EE checkbox questions to have all options checked.

example.php

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

function ee_set_checkboxes_checked() {
    wp_add_inline_script( 
        'single_page_checkout',
        'jQuery( document ).ready(function($) {
            $( ".ee-reg-qstn:checkbox").prop( "checked", true );
        });'
    );
}
add_action( 'wp_enqueue_scripts', 'ee_set_checkboxes_checked', 11 );