If you are using jQuery, why not use the validation plugin?
You should be able to combine it with a modal window (like SimpleModal).
But if you don't want to change what you have already done, try something like this:
I would just apply some CSS rules to the div to position it (I've included an overlay which covers up the page and puts the alertbox on top):
Note: The reason the div is positioned to the far left is because you need to get the dimensions of the div with the contents inside. A hidden div will have a height and width of zero. Once the size is determined, it calculates the center of the page and positions the div.
CSS
#overlay {
 position: absolute;
 left: 0;
 top: 0;
 height: 100%;
 width: 100%;
 background: #000;
 opacity: 0.8;
 filter: alpha(opacity=80);
 z-index: 100;
}
#alertbox {
 background: #444;
 padding: 10px;
 position: absolute;
 left: -99999px;
 top: 0;
 z-index: 101;
}
Script
function alertBox(alertMsg){
 // Add overlay
 $('<div id="overlay"></div>')
  .hide()
  .appendTo('body')
  .fadeIn('slow');
// Add alert
 $('<div id="alertbox"></div>')
  .html(alertMsg)
  .appendTo('body');
// calculate & position alertbox in center of viewport
 var abx = $('#alertbox');
 var abxTop = ($(window).height() - abx.height())/2;
 var abxLft = ($(window).width() - abx.width())/2;
 abx
  .hide()
  .css({ top: abxTop, left: abxLft })
  .fadeIn('slow');
// add click to hide alertbox & overlay
  $('#overlay, #alertbox').click(function(){
   $('#overlay, #alertbox').fadeOut('slow',function(){
     $('#alertbox').remove();
     $('#overlay').remove();
   });
  })
}