Here is some code using java 6 to get you started:

JSONObject jo = new JSONObject();
jo.put("firstName", "John");
jo.put("lastName", "Doe");

JSONArray ja = new JSONArray();
ja.put(jo);

JSONObject mainObj = new JSONObject();
mainObj.put("employees", ja);

Edit: Since there has been a lot of confusion about put vs add here I will attempt to explain the difference. In java 6 org.json.JSONArray contains the put method and in java 7 javax.json contains the add method.

An example of this using the builder pattern in java 7 looks something like this:

JsonObject jo = Json.createObjectBuilder()
  .add("employees", Json.createArrayBuilder()
    .add(Json.createObjectBuilder()
      .add("firstName", "John")
      .add("lastName", "Doe")))
  .build();

JSONArray objects have a function getJSONObject(int index), you can loop through all of the JSONObjects by writing a simple for-loop:

JSONArray array;
for(int n = 0; n < array.length(); n++)
{
    JSONObject object = array.getJSONObject(n);
    // do some stuff....
}

In the problematic line, instead of casting to a JSONArray, use getJSONArray:

JSONArray JSONFirewallRules = jsonObject.getJSONArray(jsonStrings.REQUEST_RULES_ALL_RESPONSE); 

However the exception isn't a cast exception, but a constructor exception where you are trying to build a JSONArray object from an unsupported list of items, which is another JSONArray :)

Something like this:

JSONObject songs= json.getJSONObject("songs");
Iterator x = songs.keys();
JSONArray jsonArray = new JSONArray();

while (x.hasNext()){
    String key = (String) x.next();
    jsonArray.put(songs.get(key));
}

org.json.JSONArray may be what you want.

String message;
JSONObject json = new JSONObject();
json.put("name", "student");

JSONArray array = new JSONArray();
JSONObject item = new JSONObject();
item.put("information", "test");
item.put("id", 3);
item.put("name", "course1");
array.put(item);

json.put("course", array);

message = json.toString();

// message
// {"course":[{"id":3,"information":"test","name":"course1"}],"name":"student"}