STYLE="Left: 0px; Top: 10px;"
This is how you would put the windows where you want them.
This is a javascript function I wrote to open a window to display information:
function info()
{
window.open("NatInfo.htm","new2","channelmode=no,toolbar=no,location=no,directories=no,status=no,menubar=no,scrollbars=no,resizeable=no,width=275,height=230,top=5,left=5"

;
}
As you can see, it uses the CSS Top and Left to put the popup window where I want on the desktop.
I hope this helps.