AWS RDS and Multiple Database Installation
Finally got it. :)

Here are the steps I took on a RDS under a VPC:


Created each Database individually on MySQL and then dumped each DB.


To log into your RDS MySQL:

mysql -h RDSEndPoint.rds.amazonaws.com -P 3306 -u MasterUser -p


To dump 

mysql -u MasterUser -p -h RDSEndPoint.rds.amazonaws.com DB_Name_on_MySQL &lt; /my/file/location/SQL_FILE.sql (You might need to change the .sql to .mysql)



Once you have your DB's set up and ready to go, change your /var/www/html/MySiteFolder/sites/default/settings.php file


To

$databases = array (
  'default' =&gt; 
  array (
    'default' =&gt; 
    array (
      'database' =&gt; 'DB_Name_on_MySQL',
      'username' =&gt; 'MasterUser',
      'password' =&gt; 'PASSWORD',
      'host' =&gt; 'RDSEndPoint.rds.amazonaws.com',
      'port' =&gt; '3306',
      'driver' =&gt; 'mysql',
      'prefix' =&gt; '',
    ),
  ),
);



You might receive this error (https://www.drupal.org/node/2394349):

Command updatedb needs a higher bootstrap level to run - you will need to invoke drush from a more functional Drupal environment to run this command.       [error]

The drush command 'updatedb' could not be executed.                  [error]

A Drupal installation directory could not be found                   [error]


You can run the following two commands on where each of your sites index.php file is located:

drush dl rules 
drush updatedb 


You should be able to see your site now! If I'm missing something I would be glad to add it for future reference.