You can add settings dialogs to individual iOS AIR applications that appear in iOS System app. It is exacty the same process as you would for a native Xcode developed iOS app - you simply make a settings.bundle file, and include with the app when its compile via ADT.jar or right from the Flash IDE and then its accessible. You then use AIR's file operations to read the results of interacting with the settings.bundle via its .plist file that is stored/updated.
For reference on creating settings.bundle files:
http://developer.apple.com/library/ios/#DOCUMENTATION/Cocoa/Conceptual/UserDefaults/Preferences/Preferences.html
Also Julian Dolce wrote a book iOS development with Flash for the Visual Blueprint label - ISBN:978-0-470-62204-9 and he covers this extensivley in several sections starting on page 260, including creating settings.bundles and all their UI options even if you don't have a Mac and xcode to work with (sinces its essentially XML files that make up a settings.bundle file),
Julian also put together some classes for the book, for reading in preferences and that is available on google here:
http://code.google.com/p/as3iphone/source/browse/#svn%2Ftrunk%2FClasses%2Fcom%2Fflashiphonedevelopment%2Fsettings
His book, although almost 2 years old at this point and a bit out of date in places because AIR has evolved so much, is still a fantastic reference filled with nuggets of good information like this. I'd also recommend Veronique Brossier's bool for OReilly - Developing Android Applications with Adobe AIR - if you are doing AIR/Android work too.
Also reference the following other threads:
http://help.adobe.com/en_US/air/build/WSfffb011ac560372f-5d0f4f25128cc9cd0cb-7ffe.html
http://forums.adobe.com/thread/928952
Hope this helps!
Rob