I have a server running webmin (different domains pointing to different app/directories). Currently I can have my php app running from a directory and all I need to do in order to make it live is get webmin to direct that domain to that specific directory.
Can I do the same with a node js app? If not, how can I use node and webmin in the same box?
I know you didn't say this specifically, but assuming you're hosting the other web stuff through, say, Apache, you would need to leverage that, but you can probably get the effect you want. Basically, it sounds like you want to be able to use "host header" separation for services, rather than having a separate IP address for, say, Apache and Node.js to each use.
So, if you let Apache bind to the main port you're using (80/443/both), then you would run ode and have it configured to listen on a different port (say 8080 as in the example you left in another comment). You can then use mod_proxy in Apache and have it route request with certain domain names to Node. Here's a: more concrete example of this but really the idea is not specific to Node. It can apply to any other process that wants to respond to HTTP requests on your server (or even on a different server).