@jkhongusc: First let me clarify a couple of things for how multisite is "supposed" to work (as in, working any other way is likely the cause of a bug or a server configuration error).
With Sub-domains
- Your main site is
site.url. This is also the entry in the wp-config.php file for the DOMAIN_CURRENT_SITE constant.
- All other sites are
domain1.site.url and domain2.site.url and so on.
- Your network admin is at
site.url/wp-admin/network/
With Sub-directories
- Your main site is at
site.url. This is also the entry in the wp-config file for the DOMAIN_CURRENT_SITE constant.
- All other sites are
site.url/sub-site1 and site.url/sub-site2 and so on.
- Your network admin is at
site.url/wp-admin/network/
Normally, you shouldn't be using a subdomain as your root WordPress installation for a multisite setup if you're going to try to use subdomains ... this would lead to strange behavior requiring new sites to be domain1.subdomain.site.url and probably won't work with your DNS setup unless you're doing it all on your own and have things set up already.
For a new installation on a .edu site with a sudomain, I would have actually recommended you use subfolders instead. Then your sites would have been http://hostname.usc.edu/site1 and so on. Now that your sites are set up, though, you can't go back to that ... well, you can, it's just tricky.
Once you have your sites living in virtual subfolders, you would use a domain mapping plugin to map your virtual hosts to the right place. So in Apache you'd keep the virtual host setup you have, but you'd install something like MU Domain Mapping in WordPress and tell WordPress which domain belongs to which site. It will handle the rest for you.
As it stands, your installation is very seriously damaged. The network dashboard URL is taken directly from the DOMAIN_CURRENT_SITE constant in wp-config.php ... so even if you try to manually navigate to http://hostname.usc.edu/wp-admin/network, WordPress will always try to redirect you back to http://usc.edu/wp-admin/network.
Your safest bet here would be to back everything up, create a new multisite installation using sub-directories and re-import your content. Then set up domain mapping to point your separate domains at the new sites.