Thanks to iOS 7 breaking my app I am having to revisit the death of making an app on windows. So I am going to blog the helpful stages properly this time round.
First up certificates of doom.
Right you need to install openssl and set up your environment variable path so you can run openssl anywhere in cmd. See here: http://www.computerhope.com/issues/ch000549.htm
Second make sure you are always running openssl as administrator. Right click run as… etc. Here is a helpful .reg edit that allows this easily: http://www.sevenforums.com/tutorials/47415-open-command-window-here-administrator.html
Next follow these steps to create your .p12 file so we can use it with Flash: http://marcosiebert.com/2011/06/ios-and-flex-4-5-getting-the-certificate-to-p12/
For APNS certs we need to create a private key with pass phrase see here: http://stackoverflow.com/questions/4294689/how-to-generate-a-key-with-passphrase-from-the-command-line
More useful openssl commands: http://www.sslshopper.com/article-most-common-openssl-commands.html
If all went well nice. Have a deep breath.
Now back in the day you had to overlay the latest Adobe Air SDK into Flash which was pretty intense and had loads of room for error. Now with CS6 you can do it via a UI. See here: http://www.yeahbutisitflash.com/?p=4141
Just before we go elsewhere you need to create all your icons and there are a lot of them. This really useful tool helps with that: http://www.gieson.com/Library/projects/utilities/icon_slayer/#.UhNhGz_3Ot4
Next we if we need to use some native extensions such as native dialog or push notifications we need to set up Flash CS6 like so: http://www.adobe.com/devnet/air/articles/using-ane-in-flash.html
Here is a very useful native extension pack: http://distriqt.com/native-extensions
Here is also a useful info on how to set minimum OS version: http://forums.adobe.com/thread/970959
Here is a useful list of what icons and launch images to include: http://help.adobe.com/en_US/air/build/WS901d38e593cd1bac1e63e3d129907d2886-8000.html
Here is also useful information on how to send push notification including certificate generation to work with PHP files: http://www.raywenderlich.com/32960/apple-push-notification-services-in-ios-6-tutorial-part-1