For ConfiGap to work you need to have your PhoneGap folder structure already created. This is an easy step if you use the Official MacOS PhoneGap App that can be found here:
Once you have set up a new folder structure using the above program you will have a confit.xml file generated. This xml file is your Source Directory.
Your Hype HTML and recourses folder need to go in the WWW folder, PhoneGap will look to run an index.html file from this directory automatically so if you name your hype file this at the beginning it b comes easier for you.
Zip the file and upload to PhoneGap Build.
Friendly reminder that if you want to preview this app on iOS you will need to provision your app / device and activate the required iOS Developer certificates. You add these as part of the PhoneGap Build creation.
iOS development preparation seems very daunting at the start, but it becomes easier. I believe that android does not require active certificates to test your app on device.
I hope to build this tutorial to explain better, but am more than happy to assist you further.
Keep at it!