Ok Carolyn,

about Google, you can't upload files of course, it needs only the URL of the XML sitemap.
In your case you have only to submit 'index.php?option=com_jmap&view=sitemap&format=xml&lang=en' in the text field for sitemaps in Google Webmasters tools.

About wrong links, i need to know from which component they get generated. By default the sitemap includes menu and contents, but can be configured also for third party extensions.

If those links come from 'content' data source simply unpublish it or exclude categories using settings.