I use PhoneGap only to build the apk (which works pretty much the same as in Intel XDK) and I add the Plugins, Icons, Splashes and so on in Intel XDK (just as I did before). It is almost the same procedure as before, but instead of building the apk inside the XDK, you get a zip which you upload to PhoneGap and PhoneGap builds your apk. Give it a try, it works well for me.