You want something like this..

JSONArray jsonArray = new JSONArray(sJSON);
JSONArray jsonPersonData = jsonArray.getJSONArray(1);
for (int i=0; i<jsonPersonData.length(); i++) {
    JSONObject item = jsonPersonData.getJSONObject(i);
    String name = item.getString("name");
    String surname = item.getString("surname");
}

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();

The problem is org.json.JSONArray will only accept String,Collection or Array but you are trying to pass the InputStream object. which is what error messages also says

org.json.JSONException: JSONArray initial value should be a string or collection or array

So first convert the InputStream into String

InputStream  inputStream = Main.class.getResourceAsStream("myFile.json");

InputStreamReader isReader = new InputStreamReader(inputStream);

BufferedReader reader = new BufferedReader(isReader);
  StringBuffer sb = new StringBuffer();
  String str;
  while((str = reader.readLine())!= null){
     sb.append(str);
  }

And then convert it into JSONArray

JSONArray myJSONArray = new JSONArray(sb.toString());

After here you can iterate the JSONArray using for loop, like here

using the following code, I hope it's help you.

//this will be your json object that contains and convert your string to jsonobject
//if you have json object already skip this.
JSONObject yourJSON = new JSONObject(targetString);

//getting the "related" jsonObject
JSONObject related = yourJSON.getJSONObject("related");

//getting the "bought_together" as an jsonArray and do what you want with it.
//you can act with jsonarray like an array
JSONArray bought_together = related.getJSONArray("bought_together");


//now if you run blow code

System.out.print(bought_together.getString(0));

//output is : D202BZX8Z6

-------update according to update the question------ you should change your code like this:

JSONObject object = new JSONObject(sampleText); //sampleText is json that has been split by line

JSONObject related = object.getJSONObject("related");

JSONArray boughtTogether = related.getJSONArray("bought_together");

-------update-------

i think you need to this point (it's not technicality all of they difference)

• every thing are in {} , they will be JSONObject and the relation is key and value like :

  {"name":"ali"}

  this is a jsonobject and the value of key "name" is ali and we call it like:

  myJsonObject.getString("name");

• every thing are in [] ,they will be JSONArray and the relation is index and value like :

  ["ali"]

  this is a JsonArray the value of index 0 is ali and we call it
  like:

  myJsonArray.getString(0);

so in your case:

1. your total object is a JSONObject
2. the value of "related" key is still a JSONObject
3. the value of "bought_together" key (which is inside the value of {jsonobject} "related" key) is a JSONArray

Have you tried using JSONArray.getJSONObject(int), and JSONArray.length() to create your for-loop:

for (int i = 0; i < recs.length(); ++i) {
    JSONObject rec = recs.getJSONObject(i);
    int id = rec.getInt("id");
    String loc = rec.getString("loc");
    // ...
}