Phil -- your question is best taken to StackOverflow (search the Cordova threads) and the push notification documentation. For example, see this doc page from the phonegap-push-plugin API docs > https://github.com/phonegap/phonegap-plugin-push/blob/master/docs/API.md < The Intel XDK creates Cordova apps, thus solutions you find related to Cordova will apply to the XDK (other than you do not have a CLI locally installed, so some instructions do not apply).
Regarding locations of sounds, I would expect those to simply be located within your project and you reference them directly via the APIs, but I haven't played with that plugin so cannot say with certainty.
Regarding which sound formats are universal, I believe WAV format is the most universal, with MP3 probably in second place.
Regarding the icons, those are going to be image resources that are added to the final package, similar to how they are added for the desktop, etc. You might have to use the intelxdk.config.additions.xml file to add them (this is a proxy for the standard Cordova CLI config.xml file).