Config files loaded twice, also How to separate Applications but share things

Hello,
I'm using "Ion Auth".

I want to have a different Application for Administration and another for Users

/admin
/application
/system
index.php (system and application folders)
administration.php (system and admin folders)

But I want to still use the same libraries and stuff in application folder (so when I update them, the administration area libraries/configs are also updated)

For example for configs.php in admin app I did this:

PHP Code:

<?php

require_once(__DIR__.'/../application/config/config.php');

// Stuff that need new value
$config['base_url']            = $config['base_url'] .  'admin/';
$config['cookie_path']      = '/admin';
$config['cookie_prefix']    = 'admin'; 


I'm going to do the same for everything shared between them.

I have two questions:
1. Is this the standard way of doing this (separating apps while sharing some files with require_once)?
2. require_once doesn't work! it seems config files (any new config file added to CI) are being loaded twice! and Ion Auth community thinks it's a CI issue (shouldn't CI avoid loading stuff if they are already loaded?)

Issue on Github (Related to my #2 Question):
https://github.com/benedmunds/CodeIgnite...ssues/1000

P.S. If you're wondering why I'm separating them, because those are 2 separate areas, I don't want any update to admin area cause unwanted issues for users or the other way around, also I can protect the administration.php file much better when it's separated, never to worry about Brute Force or anything like that.