Here's some quick code that should help you out:
Code:
$watermark = imagecreatefrompng("path/to/watermark/file/here);
imageAlphaBlending($watermark, false);
imageSaveAlpha($watermark, true);
$image_string = @file_get_contents($thumb_dest);
$image = @imagecreatefromstring($image_string);
$imageWidth=imageSX($image);
$imageHeight=imageSY($image);
$watermarkWidth=imageSX($watermark);
$watermarkHeight=imageSY($watermark);
$coordinate_X = ( $imageWidth - 5) - ( $watermarkWidth);
$coordinate_Y = ( $imageHeight - 5) - ( $watermarkHeight);
imagecopy($image, $watermark, $coordinate_X, $coordinate_Y, 0, 0, $watermarkWidth, $watermarkHeight);
imagejpeg ($image, $thumb_dest, 100);
imagedestroy($image);
imagedestroy($watermark);
Modify as needed of course.