Got it, for anyone in the same case you need to add the following script into the body (via the admin interface)
<script type="text/javascript">
Discourse.initializer({
name: 'custom-header',
initialize: function(application) {
application.registrations['app-events:main']
.on('header:show-topic', function(e){
$('#top-navbar').css('zIndex',0)
})
.on('header:hide-topic', function(e){
$('#top-navbar').css('zIndex',1001)
})
}
});
</script>