Well I just registered and have my 'main' domain working... I also have a secondary domain that I added via cPanel and the URL is the domain name...
IE...
www.site1.comwww.site2.comNow when it comes to where the 'site2' files are on the server. When you create the addon domain it will create a /home/username/public_html/site2.com directory for you to upload into. You don't have to do anything other than change the DNS server entries for your domains.