If you start with Architect, stick with Architect...
I prefer to hand code everything and this is how it's done:
*note: replace anything inside < & > below with your own stuff...
1. Create the app using Sencha CMD:
2. Modify the Sencha app code (by HAND, don't use Architect at this point!)
sencha -sdk <path to touch sdk> generate app -name <AppName> -path ./<AppName>
3. Once you've got it all worked out like you want it (test in Chrome, iOS Simulator) using localhost, then:
4. Run this within the app folder:
5. Run this within the app folder, too:
sencha cordova init <com.mydomain.appname> <AppName>
6. Open up the Xcode project under /<appname>/cordova/platforms/<ios>
sencha app build native
7. Run it!