it actually does make sense. you make a subdomain. have it point to the same directory as the main domain, and in mobile joomla's global settings, change the domain name to the subdomain (or if you have a second website that you reserved just for mobile internet, use that instead of the subdomain). in your cpanel for your internet browser, you tell it that the subdomain points to the same directory as your main domain.
we have several domains that all point to the same website right now. for a short while, we had mistakenly pointed all site names to the same directory. when someone looked at site1.com, and then at site2.com, they saw the same exact things, but the site name was different (now we simply have everything forwarded to site1.com, and when they look at site2.com, the url is changed to site1.com). mobile joomla will notice when someone with a mobile device looks at your site and tell it to go to mobile.site1.com (your subdomain). they will see your website, but it will be filtered so they see only a mobile ready website.
if that didn't make sense, how about this...
server should be set to:
domain name: site.com - directory:/main
subdomain name: mobile.site.com - directory:/main
or
secondary site name: othersite.com - directory:/main (only works if both sites are hosted on same server account)
set mobile joomla to domain name:mobile.site.com for iphone users (just an example)
regular computer users see normal website.
iphone users see iphone website