I got it working with the sqlite2 database by using 'sqlite2:' instead of 'sqlite:'
'db2'=>array(
'class'=>'CDbConnection',
'connectionString' => 'sqlite2:'.dirname(__FILE__).'/../../../thedatabase.db',
),
I can do queries like this:
Yii::app()->db2->createCommand($sql)->queryAll());
To stop Error 500 Object configuration must be an array containing a "class" element 'class'=>'CDbConnection' is required in config/main.php. I think that info is already included in the first database connection somewhere.