There are two dash board areas in a multi site version of WordPress. One is network admin area and other is domain admin area. Through a plugin I have mapped the sub domain in my network dashboard. In my network dash board I saw two sites primary and sub domain. But in my prime domain dash board I did not see both sites and only Prime site is visible. Hope I am clear.
My prime site is blogsnwebsites.com and sub domain is amazonstore.blogsnwebsites.com. The multi site plug is WordPress MU Domain Mapping.