Yes, will provide much more robust customization and control over the custom generated code. In the meantime here is an idea. Try dynamically loading and running your javascript. In your project’s <main_custom.js file add code similar to this to your phoneui.documentReadyHandler function:
/**
* Called when document is loaded.
*/
phoneui.documentReadyHandler = function() {
phoneui.loadJsAsync("http://soma.smaato.net/oapi/js/smaatoAdDisplay.js", function() {
var request = new SomaRequest();
request.adSpaceID = xxx;
request.publisherID = xxxx;
SomaTag.requestAd(request);
});
}