If a Linux system is running SuperSimpleServer hosting a tor site how does this affect the way one should achieve simultaneously using DarkMX's tor web browser based chat features to host a chat room embedded into the sss tor site?

You can use the same Tor instance with both DarkMX and SSS, no problems.

But you can't host the exact same .onion site from both at the same time.  So, a web-enabled DarkMX chat room on it's own .onion site could be linked to from a SSS site, but I don't think there's an easy way to 'embed' a DarkMX chat room into a particular page on a SSS site.  The best you could do is provide a link on your SSS site to your DarkMX chat site (and you could also customize and back-link using the Info for your chat-room, which shows up on the web view underneath the chat control.)

We'll work on some better integration between the two programs soon.  Another SSS release will come soon as well.