I don't know if I understand correctly your question and if this will help you
But this might be a solution Fiddle
<script type="text/javascript">
$(document).ready(function(){
var $container = $('#container')
var $checkboxes = $('div.tags input')
$container.isotope({itemSelector: '.item'});
$checkboxes.change(function(){
var arr = [];
$checkboxes.filter(':checked').each(function(){
arr.push( this.value );
});
arr = arr.join(', ');
$container.isotope({ filter: arr });
});
});
</script>
If this solution does not suit your needs, i apologize for making you lose time.