This is my share on Installing IonCube to your LAMP. Here are some helpful steps to follow:

(STEP 1)
# tar -zxvf ioncube_loaders_lin_x86.tar.gz
# cd ioncube

(STEP 2)
- copy the php ioncube to your server root
# cp ioncube-loader-helper.php
Go to: http://localhost/PATH_/ioncube-loader-helper.php

You should see something like this:

PHP Version ___
Operating System Linux
Threaded PHP No
php.ini file /usr/PATH_/php.ini
Required Loader ioncube_loader_lin_#.#.so

(STEP 3)
- make directory under /usr/local and paste the required .so
# cd /usr/local
# mkdir /ioncube
# cp ioncube_loader_lin_#.#.so /usr/local/ioncube

(STEP 4)
Edit php.ini file:
# gedit /etc/php5/apache2/php.ini
OR
# gedit /usr/local/lib/php.ini

- At the end of the code add this
zend_extension = /usr/local/ioncube/ioncube_loader_lin_#.#.so

Save and Exit

Restart the server by typing:
# /etc/init.d/httpd restart

(STEP 5)
To confirm that ioncube is fully working
Go to: http://localhost/PATH_/ioncube-encoded-file.php

You should see something like this:
This file has been successfully decoded. ionCube Loaders are correctly installed.

Log in to your webmin, make sure to use the user with all permisions or the super user account.

Next is click on “system” and then choose “users and groups”.
Click create a new user, enter your username, leave homedir in automatic, let webmin pick the user id, select as shell /bin/sh, click on “normal password” and choose a password, leave all other as webmin is offering, and ckick create.

Finally use any of your favorite ftp and you can now access to your FTP.

enjoy!
-Jdam