Ну может все таки так?
<!DOCTYPE HTML>
<html>
<head>
<meta charset="utf-8"/>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script>
<script>
$(function() {
$('input').change(function() {
if(this.checked) $(this).closest('div').append('<input type=hidden name="'+$(this).data('group')+'[]" value='+this.value+'>');
else $('[name^='+$(this).data('group')+'][value='+this.value+']').remove()
})
$('form').submit(function(e) {
e.preventDefault();
alert(JSON.stringify($(this).serializeArray()))
})
});
</script>
</head>
<body>
<form autocomplete="off">
<div> Group 1
<label><input type="checkbox" data-group="a" value="1" /> A</label>
<label><input type="checkbox" data-group="a" value="2" /> B</label>
<label><input type="checkbox" data-group="a" value="3" /> C</label>
</div>
<div> Group 2
<label><input type="checkbox" data-group="b" value="1" /> A</label>
<label><input type="checkbox" data-group="b" value="2" /> B</label>
<label><input type="checkbox" data-group="b" value="3" /> C</label>
</div>
<input type="reset" />
<button>Send</button>
</form>
</body>
</html>