How do I contain my JavaScript game in a div?

Question 1

As mentioned in one of the comments, a div with the id "cr-stage" is important to crafty.js. However, you don't actually have to include it. If you leave it out, it will automatically be created.

<html>
  <head>
    <!-- this is the crafty.js library, which you could load from another server -->
    <script src="crafty.js"></script>

    <!-- this is the script where all your game's JS goes -->
    <script src="mygame.js"></script>

    <script>
      window.addEventListener('load', Game.start);
    </script>
  </head>
  <body>
  </body>
</html>

If you use the above, you will get a cr-stage id created for you.

Another thing that might be relevant to your question is if you want to center the cr-stage and remove a small gap that automatically appears above it. To do that, use this code:

<html>
  <head>
    <!-- this is the crafty.js library, which you could load from another server -->
    <script src="crafty.js"></script>

    <!-- this is the script where all your game's JS goes -->
    <script src="mygame.js"></script>

    <script>
      window.addEventListener('load', Game.start);
    </script>

    <style type="text/css">
      /* remove the small gap at the top */
      body { margin-top: 0 }

      /* horizontally center your stage on the page */
      #cr-stage { margin: 0 auto 0 }
    </style>
  </head>
  <body>
  </body>
</html>

Question 2

Not sure what Game.start does. However, the script doesn't need to be in the container element. You can simply have something like that:

<html>
  <head>
    <script>
      // here some library that defines `Game.start`
      window.addEventListener('load', Game.start);
    </script>
  </head>
  <body>
    <div class="content" id="game-container"></div>
  </body>
</html>

Inside Game.start you have to use document.getElementById("game-container") in order to get a reference to the element you need, and then use that to add the nodes you want to.

Question 3

You need to give that Div an ID then modify the javascript to load the object in your div's id.