Not sure I completely understand your question, but if you're asking how to inject CSS or JS into a framed webpage in your app, the best way to do it is by using
webview (which the latest version of NW supports, and is similar to an iframe but has some advantages in my opinion).
For JS injection, see this...
https://developer.chrome.com/apps/tags/webview#method-executeScriptAnd for CSS injection, see this...
https://developer.chrome.com/apps/tags/webview#method-insertCSSA quick example...
HTML:
JS:
var webviewFrame = document.getElementById("myWebview");
// Listen for the framed page to stop loading
webviewFrame.addEventListener('loadstop', function(e) {
// Insert JS into the page
webviewFrame.executeScript({ code: " document.body.style.background = 'red'; " });
// Or insert CSS into the page
webviewFrame.insertCSS({ code: " body { background: red; } "});
});