Once you have put the values into the JSONObject then put the JSONObject into the JSONArray staright after.
Something like this maybe:
jsonObj.put("value1", 1);
jsonObj.put("value2", 900);
jsonObj.put("value3", 1368349);
jsonArray.put(jsonObj);
Then create new JSONObject, put the other values into it and add it to the JSONArray:
jsonObj.put("value1", 2);
jsonObj.put("value2", 1900);
jsonObj.put("value3", 136856);
jsonArray.put(jsonObj);