Как-то так накладывается watermark:
$src = imageCreateFromJpeg('./your_file.jpg');
$size1 = getImageSize($src);
$watermark = imageCreateFromPng('./your_file.png');
$size2 = getImageSize($watermark);
imageCopyResampled($src, $watermark, $size1[0]-$size2[0], $size1[1]-$size2[1], 0, 0, $size2[0]...