A simpler solution is to do this rather than using uniform:

$('#check1').prop('checked', true); // will check the checkbox with id check1
$('#check1').prop('checked', false); // will uncheck the checkbox with id check1

This will not trigger any click action defined.

You can also use:

$('#check1').click(); // 

This will toggle the check/uncheck for the checkbox but this will also trigger any click action you have defined. So be careful.

EDIT: jQuery 1.6+ uses prop() not attr() for checkboxes checked value

Looking at their docs, they have a $.uniform.update feature to refresh a "uniformed" element.

Example: http://jsfiddle.net/r87NH/4/

$("input:checkbox").uniform();

$("body").on("click", "#check1", function () {
    var two = $("#check2").attr("checked", this.checked);
    $.uniform.update(two);
});

$("#chkBox").attr('checked', false); 

This worked for me, this will uncheck the check box. In the same way we can use

$("#chkBox").attr('checked', true); 

to check the checkbox.