Unless there is a plugin I am unaware of, I don't believe that there is a way to sell multiple courses at once in Moodle which was your original question. It is a one by one process - but, you are correct, it would definitely be cleaner if you can keep it all in Moodle - I was just suggesting a way to extend that some - yes, it does take some extra work and resources. The Joomdle plugin provides for SSO between Joomla and Moodle and integration with many of the shopping cart plugins. It would provide a nice front for your sales.
I am not a coder but maybe someone can suggest a way to achieve a shopping cart in Moodle itself..