Sorry to hear that you're having trouble, I'm an intern at Drifty, the company that makes Codiqa.
When you select export in Codiqa, what you receive is a source code bundle for Eclipse (if you're using Android, or Xcode for iOS). Then you can load the source package into Eclipse using project import and do the signing and generate the apk the way you would any other PhoneGap or Android project.
You said you didn't compile using Eclipse, but using Ant or PhoneGap Build will be similar to building with Eclipse.
Hope that helps! :)