How do I add my deceased fathers biological deceased father to his birth certificate his mom put her boyfriends name on it and I need to prove my native American heritage and my dads biological father was native American.

You need to prove native American ancestry to qualify for government benefits or tribal membership? What evidence do you have that this man was your grandfather? You should be able to use that evidence directly to apply for the benefits you are seeking. You don't need to change the birth certificate (which would be, in any event, practically impossible to do so long after the date of your father's birth).