You can use JQuery and a plugin to do the countdown JS.

Pass the seconds in by PHP by putting it in the call, e.g.
Code: 
someDate.setSeconds(<?php echo $seconds; ?>);
Assuming the script containing $seconds is the same one which outputs the page you want to show the countdown on.

See here:
http://jsfiddle.net/8UYZP/1/

Note: in this example, I assumed $seconds its how many seconds into the future. Though you probably mean it's a unix timestamp of a date in the future.

FYI the comment in the code says one hour ahead, but its actually one day, I changed it last minute.