For instance, if you've cropped away a border, say so. Or if you're uploading a larger, but otherwise identical, version of the already existing file, write "Larger version from ", followed by the source of the new version.
Your description will appear as an edit summary; it will not appear on the file description page itself! If the new version comes from a different source, or has a different author or license, please also update the file description page after the upload.
If the new version you want to upload differs substantially from the already existing file, it is almost always better to upload the file under a new name instead of overwriting the existing file.