Sarebbe questo?
<?
$file="URL O PATH JPEG";
$file2="URL O PATH LOGO PNG DA SOVRAPPORRE";

$size=getimagesize($file);
$size2=getimagesize($file2);

$img=imagecreatefromjpeg($file);
$img2=imagecreatefrompng($file2);

imagecopy($img,$img2,$size[0]-$size2[0]-10,$size[1]-$size2[1]-10,0,0,$size2[0],$size2[1]);

imagejpeg($img,'',100);

?>

E quale img devo stampare?