I was advised to come and post this here just to let the creator(s) of Enable Multi-Site know about what happened when I tried to use the plugin. I installed it on a fresh WP 3 install and everything appeared to go fine. I used sub-folders instead of sub-domains, so I could avoid the issue with wild-card subdomains on my shared hosting.
With the main site, everything seemed fine. I got the super-admin access and menu, etc. However, when I went to setup the first sub-site it only partially worked. It installed it, but the paths (to things like the backend and theme files) all included the subfolder of the sub-site in the path, which means they didn't work.
I contacted my host, since I was advised it had something to do with httpdconf or AllowOverride. They looked into it, and this was their response:
your problem is now fixed. You did not have this line in the wp-config.php file:
define( 'WP_ALLOW_MULTISITE', true );
This actually enables the MU core within wordpress 3.0.1. Then you needed to go to Tools -> Networks and copy the .htaccess code because you were missing a whole bunch of .htaccess code as well. Clear your browser cache and you will see that this page now works and no css files are missing now
This had nothing to do with httpdconf or AllowOverride.
My understanding was that these were exactly the things Enable Multi-Site was supposed to do, but apparently it didn't work in this case, for some reason. It all works now so I'm not in need of any support, but it was recommended that I let you know by posting here. If you'd like more info, you can look at this thread where I was trying to get help with this issue.