if you purchased an audition 2 to cs6 upgrade, you should be able to install audition cs6 using its serial number and audition 2's serial number.
it's not necessary for audition 2 to be installed.
the only issue is, i don't see an audition 2 to audition cs6 upgrade path. i see an audition 3 to audition cs6 upgrade path: http://www.adobe.com/products/audition/buying-guide-upgrades.html