Using those tools is a great way to start developing your PhoneGap application if you are going to use the CLI. If you are planning to use PhoneGap Build, then you have some work to do.
PhoneGap Build only wants the www folder. The other folders the Desktop app created are not needed by PGB nor should they be upload to PGB.
Also the config.xml file is in the wrong location. It needs to be in the same directory as the index.html file.
Icons and splash screens need to be within the www folder as well. You will probably need to adjust the file paths to all of the references in the file.
Hope this starts you on the right track
creator of ConfiGAP, a tool for PhoneGap Build's config.xml file