I got to dig a bit deeper that I would have liked recently into the bowels of aegir. I needed to alter the apache site .conf file. This is a file that is controlled by aegir, so if you modify it directly. It will surely change at the next verify.
Learn from our experience using Aegir to help a client reduce their upgrade time from 2 to 3 hours to just a couple of minutes and some of the challenges we faced.
I decided to play with the AEgir deployment system and Drupal, which included Acquia, DAMP, Drush, and MAMP. Read here about my initial experiences with it.