I really can't help you without knowing what server software you're running. But I think I know what you're talking about.
For example, I own
http://www.collectivecomputing.com. We have multiple "sub domains" set up as gman2k.collectivecomputing.co
m and mooo.collectivecomputing.com. A sub domain is really just a funny naming convention like mooo.two.collectivecomputing.
com.
Your server needs to have seperate IP's for each "sub domain" and your DNS needs to be setup to direct your subdomains to the appropriate IP.
Make sence?
Funny I used to run nsync.com and can barely explain this stuff.
g00b