Not sure if it will help in your situation, but I just include files by adding the filepath at the end of my adt command line (no -e or -c). Eg (included files or bolded):
"C:\Program Files (x86)\Java\jre6\bin\java" -jar C:\Users\t.randall\Documents\AIRSDK\AIR_3.0\lib\adt.jar -package -target ipa-ad-hoc -storetype pkcs12 -keystore ..\..\Deployment\CareerBox.p12 -storepass pass -provisioning-profile ..\..\Deployment\CareerBox.mobileprovision ..\..\CareerBox.ipa CareerBox_iPhone-app.xml CareerBox_iPhone.swf AppIconsForPublish\Icon29x.png AppIconsForPublish\Icon57x.png AppIconsForPublish\Icon@2x.png AppIconsForPublish\Icon512x.png AppIconsForPublish\Icon48x.png AppIconsForPublish\Icon72x.png Default.png Default@2x.png Default-Landscape~ipad.png Data\Cards.xml Data\CareerCards.xml
It's a bit easier to stick all your files in a folder and read them out of it.. At the end of the adt command line (before any native extensions -extensionDir) is where you specify files to include. I typically make one folder and include that just by typing the name of it. The only PITA is yes, all those app icon and default startup screen filenames.
I found this page useful in working out how to package entire folders: http://help.adobe.com/en_US/air/build/WS901d38e593cd1bac1e63e3d128cdca935b-8000.html
You don't have to use -e at all. In fact I think -e is just for individual files.
Do not use 'Resources' folder. It's will not work on iOS. You can use 'Resource' but not 'Resources'