Thanks to help from Drupal Cloud support I was able to get the certificate protection to work for some of my website's page.
Now the client wants some documents linked to those pages and those document must also be certificate protected. It is my understanding that any documents uploaded and linked to the pages is findable by search engines, even if the page it is linked to is cert protected. If this is true, I need to have a way to set up a folder on the website server that will be MIT cert protected. I don’t want to have to ask them to put the protected documents on a non-drupal cloud site, kind of defeats the purpose of having everything on the new site.