Firslty you don't need to worry about the integration of jquery into html, all the things will taken care by phonegap.
And have you tried to create app using phonegap command line?
If Not then try "phonegap create yourappname", then try to build it using
"phonegap local build yourplatformname".
yourplatformname can be android/ios/wp8/wp7 etc...
you can refer phonegap
documentation for further info