If you are trying to integrate it in your current project then please go through with index.html file that will contains registerForPush function. This function is called from native android side to send device device Id generated from GCM.
Similarly when Push Notification received on Android Native side pushMessageAlert function is called that is defined in index.html file.If you go with index.html or PhoneGapActivity on Android Native side then you will find how the communication will happen between js and Android Native.
If you want to integrate in your own just define function in your main html file that are avialable in index.html file.
Let me know if more queries are concern.
Thanks & Regards