On the initial launch, AppFresh will scan your entire hard-drive for applications including Apple and Microsoft products. You will be presented with a list of applications with available updates. From then on, you can update a particular app or plugin automatically. Personally, I prefer to download the updated package and install it myself. This is to prevent any mishaps since we're dealing with a beta application.
You must be wondering how AppFresh obtains information on new updates to your application. It seeks information from Apple Software Update, Sparkle, Microsoft AutoUpdate, Adobe Updater and finally, osx.iusethis.com.
osx.iusethis.com is an interesting way for you to track your applications as well as discover new ones. There is a social aspect to it which I really like. I'm able to check out what new applications my friends and colleague are into with just a few clicks.
As for automatically updating Adobe Creative Suite and other applications by Adobe, the developers at metaquark are working hard on implementing this in a future release of AppFresh.