I figured out my self. Here you go.
1st include following line for the Header Template in the DialogPreference XML
<include layout="@layout/activity_header_template" />
and prepare own custom dialog layout just like normal custom dialog Template. The real need is, i want to customize the DialogPreference, I want two inputs for Password 1 and Password 2. (just to confirm the password)
This is my ListPreference XML code
<?xml version="1.0" encoding="utf-8"?>
<PreferenceScreen xmlns:android="http://schemas.android.com/apk/res/android">
    <PreferenceCategory android:title="@string/preference_header_encryption">
        <CheckBoxPreference
            android:key="prefkey_use_passcode"
            android:title="@string/preference_name_set_passcode"
            android:summary="@string/preference_summary_set_passcode" />
        <!-- This is how you need to attach CustomDialogPrefernce, by using the class name -->
        <!-- Please ignore title here. Title will come from DialogPreference Constructor --> 
        <com.nerds.notes.SettPassword
            android:key="prefkey_set_passcode"
            android:summary="@string/preference_app_protection"
            android:dialogMessage="@string/action_delete"
            android:positiveButtonText="@string/passcode_ok_button_text"
            android:negativeButtonText="@string/passcode_cancel_button_text"
            android:dependency="prefkey_use_passcode" />
        <CheckBoxPreference
            android:key="prefkey_app_protection"
            android:title="@string/preference_app_protection"
            android:summary="@string/preference_summary_app_protection"
            android:dependency="prefkey_use_passcode" />
    </PreferenceCategory>
</PreferenceScreen>
Following lines are very Important, the DialogPreference Constructor
public SettPassword(Context context, AttributeSet attrs) {
    super(context, attrs);
    setPersistent(false);
    setTitle(R.string.preference_name_set_passcode); // This will override ListPreference Title
    setDialogLayoutResource(R.layout.passcode_set_dialog_template);
}
Following lines should be coded in the ListPreference OnCreate Method to have custom Preference File name
protected void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    PreferenceManager manager = getPreferenceManager();
    manager.setSharedPreferencesName("Your Preference File Name");
    manager.setSharedPreferencesMode(MODE_PRIVATE);
    addPreferencesFromResource(R.xml.settings); // ListPreference XML file from XML Folder
}