My Solution. (Still need help though...)

//quiz.js
function Quiz() {
   this.quizzes = []; 
   this.currentIndex = 0;
}

Quiz.prototype.add = function(questions) {
  this.quizzes.push(questions);
};

Quiz.prototype.renderInElement = function(questions, answer1, answer2, number, score) {
    questions.innerHTML = "";
    answer1.innerHTML = "";
    answer2.innerHTML = "";

    if (number === this.quizzes.length) {
      var button1 = document.getElementById("guess0");
      button1.parentNode.removeChild(button1);

      var button2 = document.getElementById("guess1");
      button2.parentNode.removeChild(button2);

      var para1 = document.getElementById("choice0");
      para1.parentNode.removeChild(para1);

      var para2 = document.getElementById("choice1");
      para2.parentNode.removeChild(para2);

      var the_footer = document.getElementsByTagName("footer")[0];
      the_footer.parentNode.removeChild(the_footer);

      var h1 = document.getElementsByTagName("h1")[0];
      h1.innerHTML = 'Game Over';

      var h2 = document.getElementById("question");
      h2.innerHTML = 'Your score is: ';
      h2.innerHTML += score;
    }  
    questions.innerHTML += this.quizzes[number].toQuestion();
    answer1.innerHTML += this.quizzes[number].toAnswer1();
    answer2.innerHTML += this.quizzes[number].toAnswer2();
    };


Quiz.prototype.tracker = function(footer, number) {
  footer.innerHTML = "";
  footer.innerHTML += 'Question ';
  footer.innerHTML +=  number + 1;
  footer.innerHTML += ' of ';
  footer.innerHTML += this.quizzes.length;
};

//question.js
function Questions(question, answerOne, answerTwo) {
  this.question = question;
  this.answerOne = answerOne;
  this.answerTwo = answerTwo;
}

Questions.prototype.toQuestion = function() {
  //var questionPlacer = document.getElementById('question');
  //questionPlacer.innerHTML = "";
  var questionPlacer = this.question;
  return questionPlacer;
}

Questions.prototype.toAnswer1 = function() {
  //var answer1 = document.getElementById('choice0');
  //answer1.innerHTML = "";
  var answer1 = this.answerOne;
  return answer1;
}

Questions.prototype.toAnswer2 = function() {
  //var answer2 = document.getElementById('choice1');
 // answer2.innerHTML = "";
  var answer2 = this.answerTwo;
  return answer2;
}

//app.js
var quiz = new Quiz();

var historyQuestion = new Questions("Who was the first President of the United States?", "George Washington", "Thomas Jefferson");
var mathQuestion = new Questions("What is Batman's real name", "Clark Kent", "Bruce Wayne");

var answers = ["George Washington", "Bruce Wayne"];

quiz.add(historyQuestion);
quiz.add(mathQuestion);


var questionPlacer = document.getElementById('question');
var answer1 = document.getElementById('choice0');
var answer2 = document.getElementById('choice1');
var footer = document.getElementById('progress');

var number = 0;
var score = 0;

quiz.renderInElement(questionPlacer, answer1, answer2, number, score);
quiz.tracker(footer, number);

var button1 = document.getElementById('guess0');
button1.onclick = function() {
  number += 1;
  for (var i = 0; i < answers.length; i++) {
    if ( answer1.innerHTML === answers[i] ) {
      score += 1;
    }
  }
  quiz.renderInElement(questionPlacer, answer1, answer2, number, score);
  quiz.tracker(footer, number);
}

var button2 = document.getElementById('guess1');
button2.onclick = function() {
  number += 1;
  for (var i = 0; i < answers.length; i++) {
    if ( answer2.innerHTML === answers[i] ) {
      score += 1;
    } 
  }
  quiz.renderInElement(questionPlacer, answer1, answer2, number, score);
  quiz.tracker(footer, number);
}