I’ve been trying to figure out PhoneGap for about a week now and I’m just now starting to understand it because the documentation is sparse.
This is my understanding:
A PhoneGap application is a iphone safari window without the UI stuff: no bookmark bar, no scroll bar, nothing. Just a plain white canvas.
I am finding that the best starting point is to look at apple’s safari dev center to get access to the special features that safari has for the iphone like HTML5 support and the CSS3 animations.
The phonegap js library provides hooks into iphone-specific functions like touch, accelerometer, and GPS. If you do not need that functionality you do not need to use the js files.
As far as I can tell the best thing to do is make a web app first then point your phonegap application to it using the configuration file (Settings.plist). Your phonegap app is essentially a safari window that depends on your HTML and CSS to provide all of the UI because this is a safari pane, it has no navigation or address bar, or anything.
Look at the Apple Safari Dev center (http://developer.apple.com/safari/mobile.php) to figure out the interesting things that Safari can do. Do not bother looking at iphone dev, your phonegap app is really a Mobile Safari app.