Mixed subdirectory and alternate domain name sites

I am relatively new to drupal, so I apologize if I'm missing something obvious in this question.

I need to serve at least 2 separate websites with their own domain names and ssl certificates from a single webserver. For sake of discussion, let's call them foo.site.org and bar.site.org, on a server web.mega.net.
That much makes sense, but I also need to have a few sites with independent databases and settings that live as subdirectories of the server (www.mega.net/spam, www.mega.net/eggs, www.mega.net/ni, and so forth). I know it would be easier to just use new hostnames under site.org, but for political reasons, the latter set of sites have to share the mega.net IP address and certificate.

To complicate matters, having drupal manage http://www.mega.net isn't viable right at the moment. The content there was hand generated by an expensive graphical artist and removing it would be a career-limiting move.

Within these constraints, can I run http://foo.site.org, http://bar.site.org, http://www.mega.net/spam, and http://www.mega.net/eggs from a single web server and drupal installation with separate databases and without having http://www.mega.net being a drupal site as well? If so, what's the easiest way to make everything play nice together in the sites directory tree?

Thanks for listening.

Andy