When I first read your question my mind went back a time when frames were the way to do things and using links you could "target" the frame for the link. Time and web technology has moved on but you can still use the "target" for your purposes.
I know that you can name your first window using javascript
window.name = firstwindow;
And then using GET you can pass variables through the url.
<?
$yourvar = "nothing";
$vars = "10";
?>
<a href="index.php?data=<?=$yourvar?>&stuff=<?=$vars?> target="firstwindow">pass info back to main page</a>
And on your home page you can retieve those variables like so
if (isset($_GET['data'])) {$nothing = $_GET['data'];}
if (isset($_GET['stuff'])) {$num = $_GET['stuff'];}
As users don't generally like popups and as I really don't like using popups I haven't tried this but it should work unless you wish to pass large quatities of data to the first page and then I recommend using a database to hold the data temporarily and once the user exits (or on some other event) have the data deleted.