Hi there.
I just wrote a little function to zip a whole folder while maintaining the dir-structure. I hope it might help someone.

<?php
function folderToZip($folder, &$zipFile, $subfolder = null) {
    if ($zipFile == null) {
        // no resource given, exit
        return false;
    }
    // we check if $folder has a slash at its end, if not, we append one
    $folder .= end(str_split($folder)) == "/" ? "" : "/";
    $subfolder .= end(str_split($subfolder)) == "/" ? "" : "/";
    // we start by going through all files in $folder
    $handle = opendir($folder);
    while ($f = readdir($handle)) {
        if ($f != "." && $f != "..") {
            if (is_file($folder . $f)) {
                // if we find a file, store it
                // if we have a subfolder, store it there
                if ($subfolder != null)
                    $zipFile->addFile($folder . $f, $subfolder . $f);
                else
                    $zipFile->addFile($folder . $f);
            } elseif (is_dir($folder . $f)) {
                // if we find a folder, create a folder in the zip 
                $zipFile->addEmptyDir($f);
                // and call the function again
                folderToZip($folder . $f, $zipFile, $f);
            }
        }
    }
}
?>

Use it like this:
<?php
$z = new ZipArchive();
$z->open("test.zip", ZIPARCHIVE::CREATE);
folderToZip("storeThisFolder", $z);
$z->close();
?>

Have a good day!