To change icons you should change the icon files in "resources/(platform)/icon/" and splash screens from "resources/(platform)/splash/". Also there is an "icon.png" file in each platform's that needs changing and a "splash.png" in resources folder.
In addition to these, you can change the logo and various activity and other icons from "www/img/" folder. Just make sure you don't change the icon or image's dimensions.
If you want to make the app connect only to your site then edit "www/config.json" and add "siteurl" and give your site address as value to it. Oh and delete "demosites".
I hope this helps.