Change the index.html after exporting
after exporting open the index.html in Notepad++ (or some other program)
copy paste this before the </head> (you have to do this everytime you export your game)
<script src='https://cdn1.kongregate.com/javascripts/kongregate_api.js'></script>
<script type='text/javascript'>
kongregateAPI.loadAPI(function(){
window.kongregate = kongregateAPI.getAPI();
});
</script>
The Index.html should look something like this:
And that was it. You can now execute the javascript kongregate.stats.submit function in your Contruct Events and submit scores like that.