To do this simply, you would use the code you have and do what @echocode suggested, substituting field calls, for example (just using the first bit of your code)
<script>
window.onload = function () {
var onPlayergo = {
cuepoints: [
<?php the_field('custom_field_cue_one'); ?>,
<?php the_field('custom_field_cue_two'); ?>,
<?php the_field('custom_field_cue_three'); ?>,
<?php the_field('custom_field_cue_four'); ?>
],
// etc.....
