This post is more than 2 years old.
This is my third blog entry now on how to modify the default template when creating a new PhoneGap project. Previously you had to find where the default template was installed and modify it there - which also meant that when you updated CLI tools you lost your modifications. In the latest versions of the CLI tooling, specifically for Cordova, you now have a --src option to specify a source folder for your project.
In the screen shot below, I've got a folder called source. I've made a new project and told cordova to use that folder as the source of my www folder.
And that's it. Pretty simple, right? I'll be creating a good blank project for my demos and placing it in Dropbox. Note that this option does not exist for the PhoneGap CLI at this time. Finally, don't know how to check your version and upgrade? Check my blog entry here: How do you check (and update) your PhoneGap version in 3.0?