1. I am not sure if the Captive Runtime is the only option for desktop still, but I would not recommend doing it any other way. I believe that Adobe is trying to get rid of the shared runtime and there is really little benefit with the downside of having to make sure you are compatible with newer versions when they come out instead of at your own pace. Also installing you app becomes much more simple because you don't need to have any 3rd party installers to deal with.
2.The runtime .exe is made however it is a standalone app, i.e. no installer. We am only dealing with windows, so I cannot speak to a mac but we use Inno Installer to package and install and update the app with the release binaries. Basically it copies the files from the release directory and packages it into a single binary installer. 3.For updating we check the version number to webservice and if there is a newer version, alert the user. If they choose to update, the app downloads the updated Inno installer and then starts the installer with NativeProccess. The installer then updates and restarts the app. -- Sent from: http://apache-flex-users.2333346.n4.nabble.com/