So far I have successfully in setting up Aegir and seting up a number of Platforms using makefiles. Now I want to tinker with one of the platform by adding a number of modules and tweaking some template files. I realize making these changes within the platform folder will propagate to all of the sites within that platform. What I want to know is, what do I have to change, so that when I provision a new site the new modules that I have added will automatically enabled? Does this have something to do with drushrc.php? it seems there are two, one in the platform and one in the site. I'm also wondering how to get Aegir to set certain values, like auto populating users.
Both requirements (auto enable modules and autopopulating users) can be done by Drupal install profiles or distributions. Install profiles are in Drupal, not in Aegir, but fits perfectly to Aegir.
In short, I recommend you to compile your install profile and use this profile in Aegir.
See more: http://drupal.org/project/distributions