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();

There are many json serialization/deserialization frameworks available. I would recommend having a look at Jackson.

Basically, you have to create Model corresponding to json schema and deserialize json into object. Based on the example in the question, model will look like this:

@JsonIgnoreProperties(ignoreUnknown = true)
class Response {

    @JsonProperty("return")
    private ResponseObject responseObject;

    public ResponseObject getResponseObject() {
        return responseObject;
    }

    public void setResponseObject(ResponseObject responseObject) {
        this.responseObject = responseObject;
    }
}

@JsonIgnoreProperties(ignoreUnknown = true)
class ResponseObject {
    private List<Entity> entities;

    public List<Entity> getEntities() {
        return entities;
    }

    public void setEntities(List<Entity> entities) {
        this.entities = entities;
    }


}   

@JsonIgnoreProperties(ignoreUnknown = true)
class Entity {
    private String id;
    private List<Details> details;

    public String getId() {
        return id;
    }

    public void setId(String id) {
        this.id = id;
    }

    public List<Details> getDetails() {
        return details;
    }

    public void setDetails(List<Details> details) {
        this.details = details;
    }

}

@JsonIgnoreProperties(ignoreUnknown = true)
class Details {
    private String name;

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }
}

Once the model is defined, you can use ObjectMapper class to perform serialization/deserialization, e.g.:

ObjectMapper mapper = new ObjectMapper();
Response response = mapper.readValue("{\"return\": {\"entities\": [{\"id\": 2385,\"details\": [{\"name\": \"Other Known Name\",\"value\": \"John Wick\",\"match\": false}],\"proofs\": [],\"link\": \"http://domain.gg/users?id=2385\"},{\"id\": 2384,\"details\": [{\"name\": \"Discord ID\",\"value\": \"159985870458322944\",\"match\": false},{\"name\": \"SteamID64\",\"value\": \"76561197991558078\",\"match\": true},{\"name\": \"SteamVanity\",\"value\": \"test\",\"match\": false},{\"name\": \"PS4\",\"value\": \"John_S\",\"match\": false},{\"name\": \"XBox\",\"value\": \"John S\",\"match\": false},{\"name\": \"Email\",\"value\": \"[email protected]\",\"match\": true},{\"name\": \"Comment\",\"value\": \"Test user\",\"match\": false},{\"name\": \"Other Known Name\",\"value\": \"Jonathan\",\"match\": false},{\"name\": \"Reddit\",\"value\": \"/u/johns\",\"match\": true}],\"proofs\": [],\"link\": \"http://domain.gg/users?id=2384\"},{\"id\": 1680,\"details\": [{\"name\": \"Other Known Name\",\"value\": \"Johny\",\"match\": false},{\"name\": \"SteamID64\",\"value\": \"76561198213003675\",\"match\": true}],\"proofs\": [],\"link\": \"http://domain.gg/users?id=1680\"},{\"id\": 1689,\"details\": [{\"name\": \"Other Known Name\",\"value\": \"JohnnyPeto\",\"match\": false},{\"name\": \"SteamID64\",\"value\": \"76561198094228192\",\"match\": true}],\"proofs\": [],\"link\": \"http://domain.gg/users?id=1689\"}],\"notice\": \"Showing 4 out of 4 matches.\"}}", Response.class);
System.out.println(response.getResponseObject().getEntities().get(0).getId());

Here's the Javadoc.