On the checkout page, if you have created a custom field checkbox, it will be unchecked by default. If you want to have it checked by default then you can insert the following code on your checkout page:

<script>

jQuery(function() {

jQuery('#mm_custom_field_13:nth-child(3)').prop('checked', true);

});

</script>

This example is for custom field 13, you would replace that number with the ID of your custom field.