onSaveInstanceState or SharedPreferences for multiple CheckBoxes?

I am trying for a few days now to implement correctly the onSaveInstance state but with no success up til now. What am I doing wrong, as my code has no error, but there is no saving of the checkboxes state. Is it ok to implement on SaveInstanceState? Would it be better in my case with SharedPreferences? What I want is not to loose the checkbox selection on rotating the screen.Please if anyone can correct what I am doing I would be forever grateful!

Here is what I have:

MainActivity.java

package com.example.alex.savepreferencescheckbox;

import android.annotation.SuppressLint;
import android.support.v7.app.AlertDialog;
import android.support.v7.app.AppCompatActivity;
import android.os.Bundle;
import android.view.LayoutInflater;
import android.view.View;
import android.widget.CheckBox;
import android.widget.Toast;

public class MainActivity extends AppCompatActivity {

    AlertDialog dialog;
    CheckBox cbAllDay, cbBefore12, cbBetween1216, cbBetween1620, ccbAfter20;
    Boolean myBoolean1, myBoolean2, myBoolean3, myBoolean4, myBoolean5;

    @Override
    protected void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.activity_main);

    }

    public void alertDialog(View view) {

        if (dialog == null) {

            AlertDialog.Builder builder;
            builder = new AlertDialog.Builder(this);
            LayoutInflater inflater = this.getLayoutInflater();
            @SuppressLint("InflateParams") View checkBoxView = inflater.inflate(R.layout.markers_filtering, null);
            builder.setView(checkBoxView);
            cbAllDay = (CheckBox) checkBoxView.findViewById(R.id.checkBox1);
            cbBefore12 = (CheckBox) checkBoxView.findViewById(R.id.checkBox2);
            cbBetween1216 = (CheckBox) checkBoxView.findViewById(R.id.checkBox3);
            cbBetween1620 = (CheckBox) checkBoxView.findViewById(R.id.checkBox4);
            ccbAfter20 = (CheckBox) checkBoxView.findViewById(R.id.checkBox5);


            dialog = builder.create();

        }
        dialog.show();
    }

    @Override
    protected void onSaveInstanceState(Bundle outState) {
        super.onSaveInstanceState(outState);
        outState.putBoolean("CheckBox1", cbAllDay.isChecked());
        outState.putBoolean("CheckBox2", cbBefore12.isChecked());
        outState.putBoolean("CheckBox3", cbBetween1216.isChecked());
        outState.putBoolean("CheckBox4", cbBetween1620.isChecked());
        outState.putBoolean("CheckBox5", ccbAfter20.isChecked());

    }


    @Override
    protected void onRestoreInstanceState(Bundle savedInstanceState) {
        super.onRestoreInstanceState(savedInstanceState);
        myBoolean1 = savedInstanceState.getBoolean("CheckBox1");
        myBoolean2 = savedInstanceState.getBoolean("CheckBox2");
        myBoolean3 = savedInstanceState.getBoolean("CheckBox3");
        myBoolean4 = savedInstanceState.getBoolean("CheckBox4");
        myBoolean5 = savedInstanceState.getBoolean("CheckBox5");
    }

    public void applyFilter(View view) {

        dialog.dismiss();

        if (cbAllDay.isChecked()){
            Toast.makeText(this, "The first box was checked", Toast.LENGTH_SHORT).show();

        } else if (cbBefore12.isChecked()){
            Toast.makeText(this, "The second box was checked", Toast.LENGTH_SHORT).show();

        } else if (cbBetween1216.isChecked()){
            Toast.makeText(this, "The third box was checked", Toast.LENGTH_SHORT).show();

        } else if (cbBetween1620.isChecked()){
            Toast.makeText(this, "The forth box was checked", Toast.LENGTH_SHORT).show();

        } else if (ccbAfter20.isChecked()){
            Toast.makeText(this, "The fifth box was checked", Toast.LENGTH_SHORT).show();

        }
    }

    public void doNothing(View view) {

        dialog.dismiss();
    }
}

The activity main xml:

<?xml version="1.0" encoding="utf-8"?>
<RelativeLayout xmlns:android="http://ift.tt/nIICcg"
    xmlns:tools="http://ift.tt/LrGmb4"
    android:layout_width="match_parent"
    android:layout_height="match_parent"
    android:paddingBottom="@dimen/activity_vertical_margin"
    android:paddingLeft="@dimen/activity_horizontal_margin"
    android:paddingRight="@dimen/activity_horizontal_margin"
    android:paddingTop="@dimen/activity_vertical_margin"
    tools:context="com.example.alex.savepreferencescheckbox.MainActivity">

    <TextView
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:text="Hello World!"
        android:id="@+id/textView" />

    <Button
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:text="New Button"
        android:id="@+id/button"
        android:layout_marginTop="71dp"
        android:layout_below="@+id/textView"
        android:layout_alignParentStart="true"
        android:onClick="alertDialog"/>
</RelativeLayout>

and the filtering xml:

<RelativeLayout xmlns:android="http://ift.tt/nIICcg"
    android:orientation="vertical"
    android:layout_width="wrap_content"
    android:layout_height="wrap_content">

    <TextView
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:text="Choose Your Hour!"
        android:textSize="25sp"
        android:layout_marginTop="20dp"
        android:layout_marginBottom="10dp"
        android:layout_gravity="center"
        android:id="@+id/title_hour_selection"
        android:layout_alignParentTop="true"
        android:layout_centerHorizontal="true" />

    <CheckBox
        android:id="@+id/checkBox1"
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:layout_below="@+id/title_hour_selection"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:text="All day long" />

    <CheckBox
        android:id="@+id/checkBox2"
        android:layout_width="match_parent"
        android:layout_height="wrap_content"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:text="Before 12 P.M."
        android:layout_below="@+id/checkBox1"/>

    <CheckBox
        android:id="@+id/checkBox3"
        android:layout_width="match_parent"
        android:layout_height="wrap_content"
        android:layout_below="@+id/checkBox2"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:text="Between 12.00 P.M. - 16.00 P.M." />

    <CheckBox
        android:id="@+id/checkBox4"
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:layout_below="@+id/checkBox3"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:text="Between 16.00 P.M. - 20.00 P.M." />

    <CheckBox
        android:id="@+id/checkBox5"
        android:layout_width="match_parent"
        android:layout_height="wrap_content"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:layout_below="@+id/checkBox4"
        android:text="After 20.00 P.M."
        android:layout_marginBottom="10dp"/>

    <Button
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:text="OK"
        android:layout_marginLeft="30dp"
        android:layout_marginStart="30dp"
        android:layout_marginBottom="30dp"
        android:layout_below="@+id/checkBox5"
        android:id="@+id/okButton"
        android:onClick="applyFilter"/>

    <Button
        android:layout_width="wrap_content"
        android:layout_height="wrap_content"
        android:text="Cancel"
        android:id="@+id/cancelButton"
        android:layout_below="@+id/checkBox5"
        android:layout_alignRight="@+id/checkBox5"
        android:layout_alignEnd="@+id/checkBox5"
        android:layout_marginRight="30dp"
        android:layout_marginEnd="30dp"
        android:layout_marginBottom="30dp"
        android:onClick="doNothing"/>


</RelativeLayout>